Continuity mistake: Near the start, the train on the track adjacent to the train car's track is either moving or not, depending on the shot. (00:01:05)
Continuity mistake: Mulder jumps down by the fence in two configurations: one when he is filmed with a closeup (left side), and the other while he is filmed from the distance just a moment after (right side). (00:08:15)
Continuity mistake: When Senator Richard Matheson tells Mulder about the four Japanese Nationals had been murdered, he says that the murders had occurred several weeks ago. But when Mulder brings Scully up to speed a scene or two later, he tells her that someone must have been able to identify the four doctors who were performing the autopsy because they were murdered YESTERDAY. (00:30:05 - 00:33:10)
Continuity mistake: When Mulder breaks into the boat, the door shuts, but in the next shot it's wide open. Shot after that, it's closed again.
Answer: As he stated many times throughout the series, Mulder needed Scully to be sober and skeptical. Whenever Scully's skepticism wavered and she started questioning her own rationality, Mulder would try to restore her sense of skepticism, because he needed her to be clear-thinking.
Charles Austin Miller