I'm a new person with a similar problem. I looked through the forums and this was the closest thread that's related to my problem. I've only had the game on steam a week so this problem is new to me. My only question was whether or not what I was seeing was supposed to be that way or am I experiencing a glitch with the game.
I did a print screen of two images. One is of Elexis in the intro and shows her eyes are fine. The next picture is a hologram in the U4 Processing level and shows the darkness around her eyes I was talking about. Just curious if that was a stylistic thing, or is there a problem with the character or what.