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)
Revealing mistake: The guy who is jumping to the water is definitely not Mulder. It is a stunt. (00:21:20)
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)
Other mistake: It seems that the first round fired by the hit squad destroys the camera or its power supply unit, because the satellite transmission is interrupted exactly at the moment the squad enters the train car. However, the members of the squad firstly shoot in the glass and then at the doctors. (00:06:25)
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)
Plot hole: The guy who was standing at the back of the train car was somehow able to move to the front of it. This was impossible because the train car was sealed and no unauthorized person could enter it. (00:00:50)
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