Deep Throat - S1-E2
Revealing mistake: During the hard braking due to avoiding the collision with the unknown agency cars, notice that there are stunt people sitting in the car instead of Mulder and Scully. (00:21:15)
Deep Throat - S1-E2
Continuity mistake: Face-on Scully rests her elbow on the car side window frame with her wrist waving freely, while in the back shot she grabs the handle over the window (this error repeats at least three times in a row every time the shot changes). (00:20:20)
Deep Throat - S1-E2
Continuity mistake: When Mulder gives Scully the map obtained from the bartender, she holds it in her hand in different ways in each consecutive shot. (00:14:40)
Character mistake: Scully says that it was Teresa Nemman who was summoned into the woods tonight, while in fact it was Peggy Odell. (00:35:00)
Continuity mistake: Filmed from the front, Scully nods down but in the next shot when filmed from the back she still keeps her head straight and only after a while she nods it down. (00:34:20)
Continuity mistake: The place Mulder and Scully find the “X” sign is different from the place Mulder originally painted it (e.g. leafy bush, no fence etc.). (00:23:55)
Continuity mistake: When Mulder, Scully, and Dr Glass stop, in the first shot Mulder’s hands hang down and the doctor’s are in his pockets, while in the next shot Mulder’s hands are rested on his waist and the doctor’s hang loosely. (00:17:05)
Continuity mistake: In the shot taken from the front of the car Scully touches her hair with her right hand, while in the next shot her right hand rests on the car’s door. (00:10:00)
Other mistake: Being chased by Tooms Underneath the escalator, Mulder climbs out of the manhole in front of the escalator, and hits the switch to activate the escalator. Tooms is then being dragged away from the manhole, but the direction of movement of the escalator below the floor would actually have dragged him towards the manhole where Mulder and Scully are.
Continuity mistake: Just before Skinner shoots Alex Krycek in the head, Alex is lying weakly on the ground, having already been shot twice. However, as Skinner makes the kill shot, Alex is suddenly standing and falls to the ground upon impact of the bullet, with no time (or strength) for him to have risen. Also, the last shot of the dead Alex shows his face and his nostrils flare from breathing.
Plot hole: The subject of the stakeout - the religious man dressed as a female prostitute to 'put the other prostitutes at ease' before trying to 'save' them - is shown when Scully is on the phone telling Mulder about it; the man has a very masculine face, a hairy stomach and is in no way convincing. It's extremely unlikely that such an obvious cross-dressed male would fool such a large amount of people.
Three Words - S8-E16
Continuity mistake: When Mulder sits at the computer terminal in the census records room, we see two empty boxes on the screen, one for an ID and one for a password. The shot cuts to Mulder, then back to the screen and shows him typing the password, while the ID has already been typed in; it is very long and there wasn't time in between shots or nearly enough clicks of keys for Mulder to have entered that ID.
Continuity mistake: After Rob returns to his apartment after throwing out the trash bag with the bloody shirt inside, his mouth starts bleeding and he goes to the bathroom. He removes his false teeth and a few of his real teeth start falling out; he has a small smear of blood on his bottom lip when the camera is looking at him but his mouth is clean when the shot changes to his reflection in the mirror, with no time in between for him to wipe it.
Other mistake: In the police station, Scully looks twice at a photograph of one of the dead kneeling girls, whose eyes should be burned out in the photograph, but they are normal.
The Post-Modern Prometheus - S5-E5
Continuity mistake: Izzy unwraps a peanut butter sandwich and sets it on a bare tree stump as bait for 'the Great Mutato', then he steps away with the others. When we see the Great Mutato hurriedly put it down, a paper bag is suddenly sitting on the stump beside the bitten sandwich.
Revealing mistake: The dead Mrs. Sim is supposed to be nude in the bathtub, but for a brief second, a glimpse of her head and shoulders reveals the very top of a flesh-coloured modesty wrap covering her breasts. This may not be visible in a non-widescreen format release.
Other mistake: The FBI crest outside the main FBI building is incorrect as it has the words UNITED STATES BUREAU OF INVESTIGATION on it instead of FEDERAL BUREAU OF INVESTIGATION.
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.
The Pine Bluff Variant - S5-E18
Other mistake: On the information text at The Beginning of the scene telling the viewers where the scene is taking place, it is written as the "First Sovereign Bank of Pennslyvania" in "Harrisburg, Pennslyvania", instead of Pennsylvania, misspelling the name of the state both times.
Revealing mistake: When the sheet is pulled back from Mrs. McRoberts' body at the morgue, her eyelids flutter significantly despite being dead. (00:18:30)
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