Other mistake: Down in the mine, you have to put night vision on Mulder to see what is going on. Yet, without night vision, Scully can still track and follow Mulder just fine.
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.
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