In With Strings Attached, Brox looks and acts like a normal little child—until he/she starts acting his/her real age. Her/his whole mien shifts, which creeps out the four considerably.
Nebiros in New Dawn is already an outlandish looking demonic clown, barely even human looking, so it might count as an aversion, as he does not look human enough to qualify for the trope. However, it is played straight with his speaking patterns. He talks as a whole like a young teenager, has no sense of personal space, views reality as a game and is oh so enthusiastic in a very child-like way about what he does. And, suffice to say, he does not see anything wrong with being a serial killer: "Because its so fun, watching em flail about like a fishy!"
In X-Men fanfic Mutatis Mutandis, Northstar is basically described as vampirically beautiful. Rogue notices when she stares at Northstar's face for more than a few minutes, he looks so eerily perfect that he seems creepy and surreal.
In Through A Diamond Sky, Jordan takes the doppelganger issue mostly in stride...but is never entirely sure what to make of her husband's double, Clu.
The same author has Tron: Invasion (a very loose adaptation of Tron 2.0), where Jet and Mercury appear as this to each other. Jet observes that Mercury's face is a little too angular and her movements a little too precise to be human, while Mercury is vaguely put off by Jet's hair color, the lack of circuitry under his gridsuit, and the "strangely flat" quality to his voice.
In Morphic, this comes into effect in Chapter 13 after Jean accidentally "evolves," causing her face and limbs to get out of proportion. The trope title is even stated word for word.
Loopers caught up in The Infinite Loops will sometimes muse on how non-looping individuals and even nonawake versions of looping individuals are disturbingly static and predictable. On the flip side, young loopers or particularly competent nonloopers will sometimes view Loopers as strange eldritch forces inhabiting the bodies of their friends.
Invoked with Dark Tails in Sonic X: Dark Chaos, whose unblinking pupiless white eyes and emotionless features freeze Tails and Cosmos with terror during their first encounter in Episode 62. It's also completely fitting.
In The Conversion Bureau: Not Alone and its sequel The Conversion Bureau: Conquer the Stars, the newfoals are able to get sad, scared and even annoyed and frustrated, but they can't get angry or assert themselves. The natural born ponies are revealed to be unsettled by this, while the humans are just put off by how the newfoals possess their former human selves' memories and none of their original personality.
To a lesser extent, Comet Tail in the Asia Side Story finds regular earth horses to be rather unsettling and strange looking, though she notes they are still just somewhat better than the Newfoals. Another character named Sergei references this trope by name.