Continuity mistake: In the first part of the game, Mulder goes into a bathroom, and a cutscene starts where he turns around and faces a woman standing outside the door who turns into some sort of zombie. He turns to face her, with the mirror at his back. Then, when the cutscene ends, Mulder is then facing the wall and the paper towel dispenser instead of the door.
Revealing mistake: At the start of the game, Mulder goes into a diner to look for a landline phone to make a call. Going into the back, the chef is chopping up something on the stove with a butcher knife, and at this point, he's supposed to be totally fine still. Yet, as he turns his head, and if you look from the back angle, you can already see his character model has half his face burnt and part of his body burnt and bloody from lying on the stove even before he turns and is found lying on the stove moments later.