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. (00:41:35)
Continuity mistake: In the first footage of the episode we can see that the ambulance's lower right lamp is off. However, at the moment of the crash it is on. Not to mention that the Chevrolet logo, previously seen at the ambulance front, has vanished. We conclude it is not the same vehicle. (00:00:10 - 00:01:06)
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.