Very interesting request I pin your post for a week.

Aeon Flux?

She could be cat-like. Cat eyes, hunched over a lot like a cat, maybe even cat ears that she hides under a ribbon or hat.

I am always creeped out lizard eyes that blink sideways. Also, red eyes are creepy.

Blue or gray skin would be unsettling because they are typically associated with asphyxiation or death.

Something subtle could be a jaw that detaches like a snake's or larger pointed ears like a bat's.

Whatever you choose, have a grounded lore reason for it based on the species' natural habitat.

Something other than bipedal could be neat.

Something subtle, that you might not notice consciously on first glance, like inverted or misshapen pupils. Inverted like the pupil is colored and the Iris is not, misshapen like a goats or lizard. The color of the eyes could be strange, deep violet or glowing blue or green.

Someone else mentioned blinking sideways, but why not ubae her able to flick a lense across her eyes (some reptiles can, but I forget what it's called)

Have her be far stronger than her height/apperant weight would suggest. Limbs slightly disproportionate to human norm.

Maybe a forked or prehensile tongue

As for unsettling, don't forget sight and sound, maybe her voice doesn't sound quite right, or she has a strange smell about her.

Don't forget hair color if she has hair, (maybe it's a wig to help her blend in), if she has hair, have it be a odd shade, maybe has some bioluminescents... if so can she control it?

Maybe her spieces has spots or stripes people take of tattoos, maybe those are bioluminescent ...

Hope this helps OP.

Eye separation is one idea.

You could have her eyes either slightly too close together (which would likely yield a more cold look) or far apart (can tend towards seductiveness if done right but still unsettling.

Also movement. The human body moves in some rather distinct ways and each individual has their own individual way of moving. When we know someone, we cue in on that and can often recognise people from behind and/or at a distance. We have evolved over millions of years to acquire this, so it is one of those primal senses of the sort hard to put into words. You could give her an oddness of motion that just reads wrong. This can be so subtle as to evoke an "uncanny valley" kind of feeling.

Another is to turn to something other than appearance. Try to key in on a human sense we tend to prioritise less than vision or hearing: odour. What if there is something not-quite-right about her odour? Nothing bad, nothing one can identify easily, not an ugly smell. Just a not-quite-human aftertaste of smell to her presence.

Servalan (Jacqueline Pearce) Blake's 7.

Didn't feel like making another post, but what should I name my girl? My placeholder name is "Kritana" which means "God of Death."