Plot hole: After Mulder is bitten by the zombie, Scully works on making an antidote while Mulder fights off more zombies coming. Somehow, she does an autopsy on the zombie doctor, analyses the blood and toxin, and rapidly comes up with and makes 3 doses of an antidote in a mere few minutes' time. Yes, it's a video game, but that's unbelievable even for the TF2 Medic to accomplish.
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.