Character mistake: In the pause menu/inventory screen, Mulder's "Department of Investigation" ID is visible, complete with his photograph and a few other details. However, the crest and logo and the big letters that say FBI are missing from what is shown on his ID from the show.
Revealing mistake: Mulder and Scully find Katlyn in a freezer/fridge hiding, and Scully says that she's hypothermic and they need to get her out of there. As soon as the cut scene ends, both Scully and Katlyn turn to face Mulder, and their character models clip inside each other.