Continuity mistake: In The Beginning, when the Bounty Hunter gets out of his car, Jeremiah Smith says nothing. However, in the same scene at 42:08 in the "Talitha Cumi" episode, Jeremiah says "He is here to kill me." (00:00:05)
Continuity mistake: Scully tapes an X in the window,that X changes shape when Scully is talking to Mr. X and before Mr.X dies when he checks on the apartment.
Continuity mistake: Jeremiah Smith and Mulder are with the kids, and in the background, when CSM is looking through the window, Samantha's clone and the other kid disappear.
The Field Where I Died - S4-E5
Continuity mistake: When Scully is searching through the pictures to find Sarah Kavanaugh and Sullivan Biddle, she turns the photographs over and they have a label on them to say who they are. Yet when the shot changes angle to show the photos from the back, the labels have disappeared.
Musings of a Cigarette-Smoking Man - S4-E7
Continuity mistake: In other episodes the name of The Lone Gunmen's newsletter is "The Lone Gunman", but in the shots of their office door it has a sign saying "The Lone Gunmen. Publishers of 'The Magic Bullet' newsletter." (00:43:10)
Continuity mistake: The truck stolen by Mulder from the Russian labor camp is Unimog 406. However, during the accident scene, when it comes out of the woods and falls from the hill, it miraculously turns into Unimog 404 model. (00:13:30)
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)
Continuity mistake: When Scully finds out about Betts' mother she says that "She lives right here in Pittsburgh." Nothing wrong there except that at the time they has just left Chuck Burks' lab - which is in Maryland. (00:17:40 - 00:21:10)
Never Again - S4-E13
Continuity mistake: In the front shot Scully holds the photo with 2 fingers (thumb and index), while in the back shot she uses three fingers (thumb, index, and middle). (00:24:55)
Continuity mistake: When Mulder and Byers find Scully in Penny's room, there is a black stripe on the ceiling of the corridor, while in the scene when Scully is leaving the room there is no stripe there. (00:36:50)
Continuity mistake: While Mulder's waiting for Langly and Frohike to unlock the exit door, Gray-Haired Man keeps shooting at the glass door, and the increasing bullet damage on the glass doesn't stay consistent as more damage occurs, and changes between the closeups and wideshots.
Continuity mistake: While Mulder is picking himself up in the synagogue's attic after being pushed/tripped, you can see that his gun is unloaded, with no magazine. (00:25:07)
Continuity mistake: The wedding ring Ariel is holding in her outstretched hand is either vertically protruding from the palm of her hand or is hidden inside of it, depending on the shot. (00:40:25)
Unrequited - S4-E16
Continuity mistake: When Scully and Mulder run away from the dogs, the gate is fully open, while in the previous and next shot only the door is open. Plus their car standing in front of the gate is missing. (00:09:30)
Continuity mistake: During the handbrake turn Scully smiles, although in the preceding and following shot her face is very serious. (00:31:15)
Continuity mistake: In the shot of the 6th Precinct police station, it has a California state flag flying out front. The episode took place in Massachusetts, at the Massachusetts Institute of Technology. (00:07:45)
Continuity mistake: We see Scully wearing pants while sitting on the couch, but when the real Mulder comes in, she jumps up and we see she's wearing a skirt. (00:38:35 - 00:41:25)
Continuity mistake: During and just after the Mulder's seizure, when Scully's face is shown, it is at the level of a standing person which suggests that both agents are standing, but in the next shot Mulder and Scully are crouching. (00:31:35)
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