Plot hole: Scully's statement that she was 23 when she wrote her senior thesis in college throws off her timeline of college, med school, residency, FBI Academy, Quantico teaching assignment for two years, and X-Files assignment at 28. Her undergraduate degree in Physics should have been completed when she was 20 or 21 to allow at least 4 or 5 years for her medical training.
Deliberate mistake: When the unconscious, naked Asian doctor is removed from the warming tub, his hands are clasped over his crotch to protect his modesty, despite the fact that he shouldn't be able to do that, since he isn't conscious and his previously frozen limbs are now pliable and relaxed due to the heat.
Deliberate mistake: When Mulder is about to go into the metal detector he puts his gun on the counter. He goes through the metal detector on his cell phone but his keys set it off, when he steps through again it doesn't go off. No cell phones can go through metal detectors without setting it off.