Audio problem: J.T. Walsh is talking to Mulder and Scully about how smart the inmate was. During this sequence, one of the scenes has very poor audio sync. J.T. Is talking but his mouth doesn't match what he is saying. (00:07:25)
Continuity mistake: Later in the episode a man bangs on an air conditioner to try and stop it from making noise. In the first scene you can tell air is moving because the streamers are moving. After he bangs on the unit the streamers stop moving. The air conditioner is still on. (00:32:30)
Revealing mistake: When the car hits the tree, one can notice that there's a stunt sitting behind the wheel instead of the warden. (00:42:05)
Continuity mistake: During the autopsy, Scully says that the date is August 29. The two previous episodes were set in September. (00:09:50)
Continuity mistake: Ellen stays by the door looking to the right from it, but in the next shot she looks straight at Mr Incanto. (00:33:55)
Continuity mistake: The drawing image of the killer loads twice on the computer. You can see it start to load in the first shot which is closer. In the very next shot it loads from nothing again.
Visible crew/equipment: When the apartment owner comes over to the killer's apartment, she puts an envelope over near others. Right as she notices the flies, the camera tracks to the left and back. You can see its shadow cast on the wall to the left.
Continuity mistake: When the prostitute, Holly MacClaine, is first murdered, we see her face up. The next morning, when the police are at the crime scene, we see her face down.
Continuity mistake: General Callahan tells Mulder that the man he saw in his office said his name, but all he said was, "Your time has come, killer". (00:13:10 - 00:17:25)
Visible crew/equipment: After Lieutenant Colonel Stans (who has severe burns all over his body) kills Leonard Trimble, he turns to the camera, where his bathrobe is not fully covering the burn mask he is wearing, exposing a part of his shoulder and the edge of the mask. (00:42:35)
Deliberate mistake: It's completely impossible that the sound of the tape(that sounds like "Fox Maytrink") is in fact "Your time has come,Killer".
Continuity mistake: General Callahan, who is referred to as General Callahan throughout the episode by Mulder, gets called "Lieutenant" Callahan in the last scenes in the steam-room, while lying on the floor.
Other mistake: There is too much light on the ceiling for the tiny hole Amy accidentally discovers on the wall. In one shot it is plain to see that there are other light sources. (00:20:00)
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: 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)
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: 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)
Revealing mistake: The guy who is jumping to the water is definitely not Mulder. It is a stunt. (00:21:20)
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)
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