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Something is very off about this being, and everyone knows it.

Except it's not. When someone is very off, people steer clear. The creepy guy who hangs out in front of the supermarket makes his creepiness known by asking out any woman unfortunate enough to engage him in conversation for 5 seconds. The creepy little girl likes to talk in depth about dead animals she "happened" to find.

People talk and joke about creepy people they know. They do this to confirm their beliefs and to warn others. It's a form of social bonding, in a way that protects them from the weirdo...it can also be a form of discrimination.

Because there is sometimes that fine line between marking someone as creepy and discrimination, or just plain unfairness, people are reluctant to do it in borderline cases. They're more likely to label (either out loud or to themselves) when it's a stranger they won't see again, but even then, they may just shake it off.

What you want is a set of very subtle differences your character exudes. Any one of them can be passed off as misspeaking, being distracted, or just a personality quirk. It's the totality that give people pause.

Because of that, there is nothing specific anyone can point to. They won't mull over any one incident, because it doesn't amount to much. If you want all this out of not just your character's words, but also out of their thoughts, it has to be a pattern only the subconscious picks up on.

Have you ever been around someone and you suddenly start thinking about movies you saw, TV shows, books, etc? You might not even realize the person reminds you of someone else, just that hmmm, oh, this just popped into my head.

What if most every time one of your characters interacted with your eldritch, they turn to their companion and say something like, "Let's see a movie tonight! Oh, I know, how about Us?" Or they start talking about the real life haunted house in their town growing up. Or maybe they and their companion each get a quick chill.

Any one time, it doesn't mean anything. But the reader will see this over and over and get a clue, even if the characters only understand this on a subconscious level.

So what are the little things the eldritch can do that feel "off"?

I'd start with things that aren't actions or words.

People give off energy and an eldritch would have a very different energy. This would be another reason why a character wouldn't label the person as creepy or weird. Most people aren't willing to tell someone else that person's aura is off, or whatever. Unless they're already super into New Agey stuff (this is old agey stuff, but not in mainstream culture).

• Get a chill when passing the eldritch.


• When in a conversation or other interaction, your emotions feel like they're wrapped in cotton wool. You're not depressed, just muted.


• The outside world is slightly muted as well. You don't pay attention to anyone else until someone resorts to tapping your shoulder or calling your name.


• There's a pit in your stomach. Hunger? Ate something bad? Drank cold water too fast?


• You realize your child is clinging to your arm so hard you almost drop your bag.


• Your legs feel heavy, rooted, you want to end the interaction but your body isn't listening.

Then there are things that the eldritch actually does or says.

Little things they get wrong, as if they aren't from around here. There's no accent, no verbal tics, but something is not quite right. Can't put a finger on it.

• Speaks to the same to children and adults. I don't mean avoiding baby talk, but more that they don't understand that people of different ages comprehend things on different levels.


• Language is slightly too formal for the occasion.


• Aside from a couple pat phrases, a complete inability to engage in small talk. With just enough self-awareness to make people think it's a quirk, not an inability.


• No fidgeting. Nothing. No touching things to feel their texture (clothes, hair, plants). No playing with their own fingers.


• No swaying or adjusting weight (some people move because it feels right and others need to adjust weight to avoid soreness). They're not at military readiness or anything, just still.


• A second longer than average to respond to questions/conversation.


• Complete (but brief) answers to questions, no more, no less.


• Nothing personal, ever. No "my husband and I love that restaurant" or "time to go pick up the kids."


• Clothes, makeup, hair, shoes, etc are exactly so, but not looking like a professional do-over or anything. They don't look like a model or actor, but there's nothing out of place either. No wrinkles or scuffs or faded lipstick. Hair looks real and not sprayed in place, but it's not frizzy or poofy or in an off position.

Have animals react to them strangely

It's a trope (with a surprising amount of real-world evidence) that animals can sense things wrong with the world that people can't. Impending earthquakes, cancers, nefarious intentions etc.

Dogs raise their hackles and stare, cats slink out of the room. Easy to explain by him/her/it saying 'yeah, dogs and cats just don't seem to like me'. Bit strange, but hey ho. It happens to some people. Birds fly out of trees when they walk past, but birds are skittish anyway.

It's the worms that give it away. Every step on grass makes them writhe to the surface and wriggle desperately away. They touch a tree and the woodlice skitter out of the bark. Stand next to those tanks of lobsters in restaurants and they press themselves to the glass at the other end.

Yeah. Once you notice it. Terrifying.

All body movements are like would seem to just fulfill the purpose, and like a human would describe them, but they don't actually follow the physical laws of mechanics.

Essentially, the character moves like a human in a 2000s video game, but without the obvious graphics imperfections.

Most of the movements we do in everyday life are actually more complicated than it would seem. In particular, there's always a bit of counter-balancing involved against the inevitable inertial and gravitational forces. Complete absence of such movements would seem “robotically” stiff^†, that's not the case here: the eldritch does move its body in an “organic” manner, but the body is not actually made of matter that would need to observe the Newtonian laws and therefore the counterbalancing does not in fact counterbalance the initial action. Like, when they stretch out a hand, the body moves backwards a little too late to actually buffer the momentum. When they start to walk, the arms move in a way that should cause the body to twist sideways, but it doesn't.

All of the individual movements are very good imitations of real human motions, but only the “conscious goal” movements actually serve the purpose, while all the unconscious extra movements are merely recordings.

The result will be that the full-body behaviour will seem inexplicably strange to others, but whenever they try to figure out what's strange, focusing in on a detail, a single limb, they won't get behind what it is that's weird.

^†_{Actually, robots of course also obey the laws of physics. They can only get away with total stiffness when they're bolted to the floor. Newer free-moving robots actually use counterbalancing movements that look somewhat organic in a strangely uncanny way too: https://www.youtube.com/watch?v=5iV_hB08Uns}

With a repetitive bit of narrative, verbatim.

Every time someone interacts with the eldritch they:

His eyes wandering, he shuffled his feet and cleared his throat before he responded (to the eldritch).

No one ever remarks that that's what everyone does (until the reveal, and someone does figure it out), but if everyone shuffles their feet and then clears their throat when they encounter it, we readers begin to wonder wtf's up this guy, where everyone else acts kinda funny around it in the same peculiar way.

A vampire story might talk about how everyone else, 'reaches to scratch their neck for an itch that isn't there', or perhaps it's (a cliche ;) an ice elemental or the devil, and everyone (thinks they), 'feel a draft', from doors, windows, or floor boards (different things, so as to make it less obvious).

As I interpret your question, you're not interested in specific behaviors or traits that will mark the person as alien.

Though, they seem for all appearances and seemingly all mannerisms to
appear as human, they are not. The human eyes, but not mind, are
fooled. Something is very off about this being, and everyone knows it.

The characters instinctively, and maybe even consciously, understand that this other character is an eldritch abomination despite their behavior and appearance being entirely normal.
You just want to know how to convey this to the readers without outright saying it.

So, here's a few ideas:

• Change your writing style when you're describing them. The descriptions can remain factually the same, so that the character's behavior is not necessarily different from that of any of the other characters, but the way you present them will be subtly different. Make the sentences describing the character's actions longer, more stream of consciousness. Make them shorter. Break them up. Into smaller fragments. Use certain words to describe them but not other characters. Maybe their shirt is verdant, even though it's the exact same shade as another character's green shirt. In this manner, the readers will get a sense that something is different about the character, even though nothing observable actually is—the same sense that the other characters in the story have.


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  Don't change their behavior or appearance. Change what happens around them. Alter the probabilities a bit. They react just the way any number of people would have act when confronted when they're almost hit by a car, or mauled by a bear, or when they win the lottery. Of course, it's awfully strange that all those things happened on the same day, but they did remark on what a crazy day they had, just as you'd expect...right?

  
  
  

  Or whenever they hear someone say their name, even if they're not addressing them, they turn their head (or don't turn their head, or any number of the other things people do). But you start to realize that it's strange how many times you hear someone mention their name, especially considering that it's not really all that common, when you think about it.

  
  


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  Change how other characters react. Other answers have mentioned things along these lines, but maybe people's behavior is subtly different around them, something you can hint at in the text. For something like this, it would be good to have a foil who behaves mostly the same way, but doesn't elicit these different reactions, so that people don't just assume it's something idiosyncratic. For example, if they're a businessperson, they act and look much like the businesspeople in the story, but for some inexplicable reason people act different around them.

  
  
  

  How do they act different? Maybe they say they love this person's company, and maybe they even act like they do, but they always seem to be in a hurry to finish talking to them. Maybe they're unusually honest around them, despite not meaning to be. Or always in a bad mood but they're not sure why. In other words, however other people normally behave, they inexplicably don't around the eldritch abomination.

  
  


• This might not be what you're looking for, if you really want there to be nothing odd about their appearance. But, along the lines of appearances, you say they appear as human. But do they always appear as the same human? Maybe their face is a little different every time the characters see them, something that could be conveyed by descriptions. Maybe it's the opposite: they're always the same height, even though it should have changed a bit over the day. Maybe they're very good-looking—no surprise there, attractive people exist—but their face is more symmetric than is physically or probabilistically possible for a human being.

What you're describing is basically Uncanny Valley, which is a fairly active area of research.

As leftaroundabout says in his answer, this has clear implications for CGI. If you want your CGI to model a monster of some kind, we don't have a mental map of how that should work; but for humans we do, and mismatches are jarring on an instinctual level. Even with CGI, it may appear statically correct and may even articulate correctly, but some other factor makes it behave incorrectly. Even in 2019 when we're used to film-quality CGI with fully CGI creatures and humans, the current state of the art for CGI is still unable to correctly model a flying creature landing which looks realistic to anyone who's ever looked closely at a bird.

This has implications beyond CGI though as people start thinking about androids, or about telepresence in android bodies. CGI is a good start, but it doesn't necessarily follow through to a physical body you're close to. Hiroshi Ishiguro has done some particularly interesting work here.

As for how to describe it, all the literature on Uncanny Valley gives you many ways in which appearance can be "off" and ways to describe its effect.

Demonstration

All humɑn beings ɑre born free ɑnd equɑl in dignity ɑnd rights. They ɑre endowed with reɑson ɑnd conscience ɑnd should ɑct towɑrds one ɑnother in ɑ spirit of brotherhood. — Universɑl Declɑrɑtion of Humɑn Rights.

Ideally that text would have invoked a subtle feeling of oddness since:

every normal (double-storey) a has been replaced by a single-storey ɑ. I here abused a Unicode character intended for phonetics to achieve this effect. Therefore, the effect may have been spoiled if the font in which this text was rendered for you sucks at supporting special characters (or you are using a screen reader or other non-standard ways to consume that text). Otherwise, if you directly noticed what was odd, you are very observant in this respect.

Actual Answer

If you want to invoke a feeling of oddness directly in the reader, you can use slight typographic differences for every word said by your eldritch being (or if it does not speak, when describing its actions).
Since parsing text happens mostly automatically for most of us and we are also very good at autocorrecting if something is slightly off, the reader may not consciously notice such changes, but only be slightly unsettled by them subconsciously.

Possible changes are:

• Switching between common variants of a letter such as single-storey and double-storey a and g. Some modern typefaces offer variants of several other letters as well, some of which can be very subtle, such as the the letter g missing its ear.




• Switch between a matching pair of serif and sans-serif typefaces. There are only few pairs of typefaces that are so close that this may works.




• Similar to the above, mirror or or rotate every instance of such letters as A, H, M, S, O, V, W, X, Z, o, s, v, w, x, z. Whether this actually makes a difference and is sufficiently subtle depends on the typeface. For example, my browser renders this in a typeface where I can only spot (very subtle) differences for H, S, and s.




• Slightly change the kerning, i.e., the spacing of letters. (Credits to Leftroundabout.)

The last two are the most difficult to pull off, but have the advantage of not only being a different style choice but being actually subtly imbalanced.

The downsides of this approach are:

• Accessibility and portability are considerably diminished or require effort.




• It does not have the same effect on every reader: A typographically predisposed reader may instantly notice what is going on, while others may not notice it at all. But then this applies to almost every literary technique. To some extent, you can compensate for this with slowly driving up the intensity, so that it will go from unnoticed to subconscious to explicit for every reader, just at different points in your story.




• Unless you are using something like TeX, the act of writing this may be tedious.

Instinct warns your other characters that there is something other about this one. He has never been observed to lose his temper in situations where that would be expected nor has he exhibited fear when that was appropriate.

You say everyone knows it, so the occasional Jesse is weird comment or thought would not be unusual. You wish to avoid this, so the tone with which you write this character can be the clue.

He can show no strong emotion since as an eldritch being angry or fearful would render him lethal to the world. He charts a middle course and seems to feel little, certainly no strong emotions. He says little and what he does say is slightly inappropriate to the situation. Eldritch beings don’t need to do research and study human behaviour, so his will be ever so slightly askew.

Perhaps one thing that he has done is make it so others are unable to discuss him. He cannot be a subject of conversation as that is one way he has chosen to protect himself from discovery.

I would try the occasional scene where Jesse is present and even pivotal, but in later conversations about it he is not mentioned as having been present and his role was performed by someone or some guy who they just can’t remember - or by the speaker, but the other party knows this is not how it happened but can’t correct him as he cannot think about Jesse either.

Perhaps some have known him for years and Jesse does not change, forgetting to age his appearance. Perpetual thirty-five year old, but no one ever notices it unless in his presence and upon leaving, forgets.

I don't think any of the other answers has covered that this is really a point of view question. Your eldritch character doesn't need to look different, act different, have funny traits or even speak in a different typeface. In fact, it's perhaps better if there's nothing identifiably odd about him at all. Just make your point of view character inexplicably creeped out by him. Your reader will follow along.

As far as how you depict this, you have a wide range of options. If it rises to a conscious level for your POV character you can put it in an internal monologue:

"I don't like him," Marjorie thought to herself. "I don't know why, but I just don't like him."

or describe your POV character's reactions

It was hard not to be charmed by his wide blue eyes and sunny smile, but Marjorie felt a little cold shiver down her spine every time he looked her direction.

Or, if you want to ease it in at a subconscious level, you can color the descriptions

He was beautiful, but was there a certain emptiness behind his eyes?

Or be yet more subtle still

His eyes were the exact blue of a desolate, lonely sky.

The key is to remember that the point of view informs the descriptions. This eldritch character is very good at fitting in. So there isn't anything really about him that's a solid clue. Your POV character is just sensing something off through raw intuition --and that translates to the reader. You can tweak it to be as subtle or as blatant as you want.

In addition to what others have mentioned, I think you can achieve a lot with creepy oddities about the face.

Eyes

• Not blinking (or less frequently, the eldritch probably realizes this is something people do)


• Looking at you straight without having the eyes dart around


• Lack of reflection


• The eyes show up weird in photographs (i.e. they always have red eyes)


• The pupils don't adjust to brightness, or are always too wide/small as if they were on drugs


• The iris is of inconsistent color (every time you look at them you go, "I could have sworn they had blue eyes")


• The eyes don't change to match their apparent emotions.

Nose

• A tendency to flare their nostrils (sniffing, breathing, or in reaction to something)


• Weird sounds when breathing


• Or alternatively, breathing is completely silent, which (breathing generally being quiet) only seems weird by the complete absence of noise

Mouth / Speech

• Hardly opening their lips when speaking (like a really good ventriloquist)


• The shape of the mouth is subtly "wrong" (too wide etc.)


• No smiling. In general, the shape of their mouth doesn't change to match their apparent emotions.


• You hardly ever see their teeth or tongue (even when they're eating something)


• When you do see the teeth, there's something subtly wrong (teeth too straight, an unnatural gleam, etc.)


• They don't show the mannerisms other people do: licking or nibbling their lips, gulping, or even yawning.


• No stumbling over words, pauses looking for words, etc. Each sentence sounds like from a written speech. (But they may take breaks between sentences to construct the next one.)


• Their laughter always sounds the exact same way

Things change, things that shouldn't.

In one scene they have blue eyes, some time later, they are grey.

A tattoo that used to be a bird now is shows a flower.

Their hair grows from short to long in way too short time.

Their clothes change when they really have had no opportunity to change them.

When they need some item, they already have it in their hand. Always.

Brandon Sanderson uses shadows which point the wrong way, towards the light instead of away, in at least one of his books to mark when something is wrong.

Maybe your being should similarly warp physics in various subtle ways?

• When he speaks, things close to edges on counters tend to fall off.


• Water won't boil when he is present.


• Gravity seems weaker.


• They leave the room, but are still present. "As X was explaining the situation, Y sat up straight, and Z, seemingly bored, left for his bedroom. X asked Y if he understood what was just said, so Y gestured to Z and asked "Z, what do you think?" To which Z responded, "I'd say it's straightforward".

Your premise is not fully fleshed out.

What do they want?

Why are they in human form?

Why/how are they creepy? if they wear a human guise to fool humans, why would they be so creepy? They need more practice playing the role of humans?

The mind is actually easier to fool than the eyes.

What is not so easily fool is our animal instinct...

So we sense something is wrong... and yet people ignore that.. why? because our mind and our eyes override that instinct.

Are they beautiful? Do they look of promise of something?

when you have fleshed out their motivations and their power (and limitations) of their disguises, their creepiness will fall into place.

The specific details you choose don't matter as much as how you wield them. You want to start out with details that are incredibly subtle. These are less to clue your readers in and more to reward close readers and give "aha!" moments on rereads. Then, move to details that are more noticeable but don't give a complete picture so that your readers start actively guessing what's going on. Gradually increase how blatant the hints are. When you're ready for your monster's identity to be clear, give a final clue or two that ties the whole riddle together for your readers.

One of my favorite examples of this is the main antagonist in Terry Pratchett's novel Reaper Man. It's set up the opposite of your question - it's a blatantly eldritch being with a mysterious and surprising true nature - but the progression of hints is similar to what I think you'd find helpful.

In the story, mysterious snow globes begin spontaneously appearing. They're clearly introduced as being a threat, but what exactly they're doing is left as the mystery that's gradually built up. People who find them start selling them, causing the globes to be distributed around the city that makes the main setting. This is as much the globes' decision as it is the choice of the people trying to make money. This doesn't tip Pratchett's hand in the mystery yet, but when you know what the globes truly are, this makes a lot of sense. It is a deliberately obtuse hint that gives a nice "aha" moment later in the story.

Eventually, the globes hatch and turn into sentient metal carts, which wheel around and cause havoc around the city. Now the clue is impossible to miss and gets you to start thinking. Shortly before the climax, the carts begin congregating near some kind of hive that has just appeared outside the city, and pamphlets of paper advertising new businesses opening up inside the hive start raining from the sky. It's pretty clear at this point that the hive is some kind of predator that wants to lure human victims inside of it, and the carts are its drones. The puzzle pieces start coming together, but the picture is still muddy.

The final battle begins as the protagonists go inside of the hive. The hive is described in lovecraftian language. It's made of large, cavernous hallways that are fleshy but quickly solidifying into some sort of cathedral-like building. Strange words appear on walls. The humans the hive has already consumed have been put under its thrall and forced to dress as guards or clowns. At some point in all of this description, it hits you:

The "hive" is a sentient shopping mall, and the carts are actually just shopping carts. If the mall wins, it's going to suck the life energy out of the city it's attacking - by turning it into a boring cookie-cutter shopping district!

The way Pratchett handles this build-up is so masterful that he does not refer to the hive's true identity until several dozen pages after the reader has figured it out for themselves, and the way he finally calls the monster by its true name is so casual that it's clear he's confident the reader is already in on the secret. I do recommend reading Reaper Man for a strong example of how to present a mysterious antagonist and give the reader a sense something is off, but not give away exactly what they should be suspicious of until the story wants it to happen.

There was a short story I read a while ago, where a character was clued in to some mental meddling by another character answering a question word-for-word the same on three occasions in the text, with none of the little variations people toss in or without (apparently) realizing or commenting that they'd already answered. The questions were far enough apart, and the answers casual enough, that it wasn't obvious, obvious, but it could've been enough to be noticed (or even not-noticed, but make someone twitchy) before the character brought it up.

So, maybe you could have some... echoes in people's POVs about this character. Little sentences or fragments or observations that just happen to be word-for-word the same across some otherwise different POV's - because the perfectly ordinary responses to perfectly ordinary actions by this character are, well, in universe scripted out.

If the POVs and the characters are otherwise not overly similar, ie, wouldn't use the same phrasing or vocabulary, it wouldn't come across as "just" reusing phrases but could create a subtle flatness or repetition that could be unnerving.

This would pair exceedingly well with Wrzlprmft's suggestion of playing around with subtle linguistic changes - using subtly different or altered versions of characters or fonts when referring to this person, to give a subtle sense of difference.

If, or maybe when, you need to make it increasingly obvious, you could have characters begin to notice similar turns of phrase - but not (at first) think anything of it... maybe a glance to the last person who said the exact-same-thing in the last scene, maybe a half-smile when it's echoed since it was expected, or someone "quoting" rather than saying the phrase, or more than one saying it in unison (again, possibly "on purpose")... there are reasons people might use the same phrase (usually quotes or inside jokes), so it can be subtly noticed and called out without becoming overt right away, and only later escalate into this echoey mindless repeat of a phrase even when it's clear it doesn't apply the way it seemed.

Too much detail

Any time I wish to make the reader uncomfortable I start describing things or people with too much detail. Human beings are great for that because when we observe people we see them as a person. We are so used to humans that the pile of talking meat does not seem weird to us at all. Now on the other hand if we lets say see a robot, a 1960s robot with huge pistons and nothing human shaped it may very well come apart in our minds into mechanical parts.

So this is what you do, have the narrator see this person as a pile of meat instead of a person, because that is what they are.

How do you execute this? Start by reading your anatomy books. Humans have lots of parts and muscles and it's great time to mention them.

here is an example. Normal person

"I want to go the store," Bob said.

VS

Bob sucked air into his lungs filling the alveoli. He then opened
his mouth showing a pink tongue shining from saliva. The pushed air
through the taught chords pitching the sound into distinct noises. His
lips tightened and relaxed further adding modulation. A sound came out
audible to human hearing, "I want to go to the store"

Creepy normally scare people away. Maybe its just their eyes that are an issue not counted as murderous but just don't look straight into them. As someone who has a family trait of both resting bitch face and murderous eyes when all I'm doing is just my normal neutral expression it does turn some people off I look at people who are joking and they'll think they've deeply pissed me off and apologize or go quiet and all I did was just glance up and go back to work. For me this can be a bit weird how they react to that. Odd jokes is another way like finding humor in death, mutilation, or car crashes ect but combo the looks and jokes too often and some people do want you to be evaluated.

It could just be an air about them that only a very rare few people could pick up on. Or people feel the slightest of dizzy spells that they could blame on a million other things but never this one character added to that its not enough of a spell to want them to sit down or fall over.

Or the character is very friendly when approached yet they do not approach others but people are simultaneously drawn to them when they are of a vibrational tune this eldritch finds comforting or whatever the person however may take on a mannerism they've never done like itch their ear or like a flavor or color or think x is more x when they hang out with eldritch. Assuming your eldritch is suppose to blend in with society.

Someone eventually points this oddity out to the main character it takes several times the person pointing it out is not of the same vibrational patterns the eldritch likes so they don't get along eventually through great effort the main character begins to learn they do the thing and questions why. If the MC starts to change the pattern they change their frequency souring the eldritch to them.

I think a character that did well in hiding their serial killer tendencies was the villain of Life is Strange no one thought it was them by a lot of accounts and many were shocked it was them but once you replay the game it was there all the time it wasn't his eyes mostly it was what he said and how he said it and knowing what you knew its like right in front of you the entire time but the game had you thinking it was several other people to the point you got to joking is the killer that millennial snob there or the janitor? Or was it that awkward guy who knew the murder victim and wanted to sketch you?