Possible ideas for that could be if the enemies in one act that aren't real use the base art style from another act. This would use the existing art from the game, but still make the enemies seem out of place.
Except the art styles of all chapters are the same, to save on resources, and the difference in colour and tone is enforced by lighting and screen filters.
Another idea would be if you occasionally flickered these enemies, with enough subtlety so it's not too apparent they're unreal, and just frequent/seldom enough so the player doesn't notice it as soon as they see the enemy.
This isn't something that can't really be done without alerting the player or making them thing the game is bugging out.
Another would be if the unreal enemies are very subtly blurred.
Let me tell you how the player would react to this, with how this game works.
"Ah, shit. What's going on with my perception?" *Opens up the menu, spends the next fifteen minutes trying to figure out which of the listed effects is lowering their perception, eventually decides it's the enemy. "So this enemy type lowers my perception when I look at it? Whatever, it's not a strong effect."
Yeah, I know, I never mentioned the perception attribute (or any of the other nine, for that matter) or how it works, but if the enemy is blurry they'll think it's a perception hit, and their thoughts will go no further.
Or shifting the colors of the enemies so they look a bit off, but still believable and fitting within the act.
That may well be part of tweaking their art style.
These ideas shouldn't be too taxing neither on the art designers, nor the programmers to implement, but it's up to you and your team to decide if any of these would work/fit.
But none of them work as well as tweaking their art style. Like drawing war and his blind soldiers like they're in a political cartoon. I'll take this to visual arts.