Continuity mistake: During the shootout in the warehouse, a wedding ring is visible on Mulder's finger. While it's possible Mulder was married before, the Lone Gunmen are shown hacking into Mulder's FBI dossier and Langly reads out that he is single.
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.
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 toxicology report lists the birth date of Mrs. Sim as 6/6/67 which would make her 30, but Detective Kresge says that she is 40 years of age. (00:03:45 - 00:14:10)
Plot hole: On the phone, Scully asks for the report on her sister to be sent to the San Diego F.B.I field office (since she is visiting her brother and his wife and so is not in Washington), but the package is sent to her brother's home. Even if 'Danny,' whom she asks for the file, decided to be helpful and send it directly to her, her brother's address is not likely to be the one in her personal file, plus she didn't mention that that's where she'd be staying.
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.
Continuity mistake: Mulder says that Scully was abducted and missing for four weeks. In "Duane Barry," the date stamp is given as August, then in "3," when Mulder returns to the X-Files office he turns the calendar all the way to November. Since Scully is returned the next episode after this, she must have been missing for at least 3 months, not 1. (00:06:20)
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)
Kitsunegari - S5-E8
Revealing mistake: When Scully pries open the mouth of the man who died from being forced to ingest paint, his eyes twitch. (00:13:50)
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)
Schizogeny - S5-E9
Revealing mistake: A heavy rain is falling but there is no sign of it on Mulder and Scully. (00:32:00)
Kill Switch - S5-E11
Continuity mistake: In the same season episode "Unusual Supects" Fox Mulder's file lists him as Fox William Mulder. The A.I. discovers a similar file but the name is just Fox Mulder.
Visible crew/equipment: I don't know if this is visible in all formats, but on the newest UK release on DVD, watching in widescreen, it's amazingly obvious. When Mulder recovers from the vampire attack, he gets up from the floor and breaks up a chair to make a stake. There is a shot of his feet as he smashes the legs off and bends to pick up a piece. In the bottom left hand corner of the screen, you can see a crew member's hand carefully and quickly placing a piece of wood on top of the pile for Mulder to pick up.
Revealing mistake: When the doctor examine Ronnie's "corpse" in the morgue, he pulls out the stake. It is quite obvious that he's struggling with a wooden stake that is placed on the actor's side, not through his chest. Moreover, the camera pans up and you can briefly see Ronnie's unharmed chest.
Continuity mistake: In season 2's "Ascension," Skyland Mountain was a private ski resort, yet here we are told it is a national park. (00:25:10)
Continuity mistake: Uroff-Koltoff Star of Russia in New York Harbor is a completely different ship from Uroff-Koltoff Star of Russia leaving Vladivostok at 17:45. (00:33:10)
The Red and the Black (2) - S5-E14
Revealing mistake: It seems that in the first shot the doctor injects something into the vaccine vial rather than extracting from it since the syringe plunger is moving inwards instead of outwards. In the next shot one can see that the syringe is being filled with the vaccine, however the arrangement of doctor's fingers is suitable for injection, which strongly suggests that the scene is played backwards. (00:17:55)
The Red and the Black (2) - S5-E14
Continuity mistake: While in the car with Scully, Mulder turns his head aside of Scully towards the side window twice: once when the shot is facing Scully, and just after in the shot facing him. (00:40:25)
Character mistake: While examining Agent Michel's body, the doctor says to Arthur Dales about "toxology report" instead of "toxicology report." Toxology is the study of archery. (00:26:50)
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