Visible crew/equipment: When the Lone Gunmen catch up with Suzanne at The End of the episode, when she is talking to them and the camera is on the three, you can see not one, but two boom mics at the top of the screen. (00:40:20)
Schizogeny - S5-E9
Continuity mistake: After her father is pulled out of the window, Lisa leans out and there is no glass left on the sill, she even places her hands on it. Later when Mulder and Scully look at it, there is all sorts of jagged edges on the sill. (00:16:35 - 00:20:00)
Fresh Bones - S2-E15
Revealing mistake: While Mulder, Scully, and the groundskeeper are walking through Folkstone Municipal Cemetery, there is a partially hidden but still conspicuous sign that reads "Vancouver Cemetery." (00:18:45)
Continuity mistake: When Fox Mulder is having the flashback when Samantha was abducted, he looks at the doorknob, in the close-up he is still looking at the doorknob but it has changed colour.
Sanguinarium - S4-E6
Revealing mistake: When Mulder and Scully enter the doctor's house, you can see over their shoulders that it is showering with rain outside, yet both of them are bone dry.
Continuity mistake: Scully's FBI badge number that she gives to the phone company is different to the one she gives in season 4's "Teliko". (00:02:05)
Continuity mistake: The dates on the academic discipline and progress forms for Max are not in accord with the order of the episode, coming after the "Millennium" episode. Supposedly the changes in his behavior and grades started a few months before, but the reports are from a few years ago. (00:24:55)
Continuity mistake: After Mulder has been released from the containment cell, and he and Scully go back to his room, the items on the table change position in between shots. (00:15:00)
Anasazi (1) - S2-E25
Other mistake: Immediately after a shot has been heard, Mulder, who is in flat #42, grabs his gun and rushes through the corridor passing by flat #47, which means he is still on the same floor. Within 10 seconds after the shot, the next-door lady is already aware of the crime. Not mentioning that 2 seconds later two policemen arrive at the scene. (00:07:21)
Plot hole: The ability of the Faceless Rebels to impersonate other people completely defies logic. For one, when impersonating someone, the Faceless Rebel is able to speak despite the fact that they mutilate their own mouths shut. Secondly, as can be seen in many instances when a person is being attacked by a Faceless Rebel, the face of the person they are impersonating is merely a skin mask that can easily be pulled off. If the face of the person they are impersonating is just a mask, then any time a Faceless Rebel speaks you should be able to see their true face through the open mouth of the skin mask. Additionally, the face of the person being impersonated being a mask would also preclude the Faceless Rebel from blinking or moving the mask's eyes (similarly they mutilate their own eyes shut, so the eyes of the skin mask can't be their own).
Character mistake: When Mulder and Scully are in the graveyard, the headstone says "Howard Patrick Graves", but the newspaper said his middle name was Thomas.
Continuity mistake: When Dr. Kendrick/Eve is talking to the two little girls and she's clearing up the mess on the table, the position of the straw changes between shots. (00:29:55)
Kitsunegari - S5-E8
Continuity mistake: How was Modell tried and convicted in 1996 if he only woke up six months ago? Six months before this episode would be at least mid 1997. (00:06:05)
Field Trip - S6-E21
Continuity mistake: At Mulder's 'funeral' around when there is a knock at the door, we see Frohike raise his bottle to take a swig. The shot cuts to facing Scully and we can see Frohike further in the background and his bottle is nowhere to be seen, when he should've been mid-swig.
Visible crew/equipment: While Fox is fighting the agent in the underground garage you see a crew person on the right side of screen for a split second. (00:38:55)
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)
Other mistake: When Mulder opens the body bag containing the "partial" remains of Max Pfennig (AKA Paul Gidney) a pulse can be seen beating in the right side of the corpse's neck. (00:18:10)
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