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)
Factual error: The date stamp says that it is April 12 and Scully says that it is Sunday, but April 12, 1997 was a Saturday. (00:03:10)
Factual error: The townspeople contracted Creutzfeldt-Jakob disease (CJD) from the bodies they consumed and it showed up in the brain tissue within a matter of weeks. However, this extremely rare disease takes several years to even be detectable. (00:18:55)
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.
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.
Anasazi (1) - S2-E25
Visible crew/equipment: As Scully stands up to leave at the offices of the Navajo Nation, the reflection of a boom mike moving in one of the picture frames on the wall can be seen. (00:19:40)
Factual error: Mulder says that the events occur near I-10, however, I-10 is nearly 200 miles south of Arkansas's border in southern Louisiana.
Continuity mistake: When Martin takes out the nanny-cam from the bear, the lens-protection is on so the camera could not have recorded anything. (00:30:00)
Continuity mistake: When Mulder and Scully first see the artifact rubbing in Skinner's office, the rubbing is quite faint and lightly done. A couple of times during the episode, the rubbing becomes darker and heavier drawn.
Continuity mistake: When Scully arrives to investigate the kid who was crushed by the bleachers the time stamp says 5:10AM. It seems strange that the investigation would start the next morning, unless the high school holds basketball practice at 3:00 in the morning. (00:16:35)
The Sixth Extinction (2) - S7-E1
Revealing mistake: When Scully enters the F.B.I. Building after returning from Africa, she isn't wearing her badge. She'd need it to walk around without being stopped by security. (00:35:50)
Continuity mistake: If the Kernoffs were really devoted Catholics why would they have waited six years to have Dara baptised? (00:00:40)
Factual error: Mulder calls the dust in Maleeni's van "lycopodium powder" that the Los Angeles Police Department used to collect fingerprints, but the real LAPD uses latent print powder not lycopodium. (00:06:35)
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)
Invocation - S8-E5
Continuity mistake: When the psychic collapses, sun is streaming through the window, indicating early afternoon. When we see the ambulance driving away a few scenes later, it's dark outside. It's highly unlikely it took a medic team several hours to get there and stabilise her.
Continuity mistake: In the scene at the start, when the police car passes the truck, clearly it is daylight, but right after the truck shuts down it is completely dark. (00:03:25)
Continuity mistake: Mulder recalls to Scully that he saw Krycek being pulled out of the car and then saw the bright flash, but he only came to just in time to see the flash. (00:08:50 - 00:12:00)
Continuity mistake: Randall has strange pale eyes but just before he shoots Dwight, when he is aiming the gun at Tammi, there are several close ups of his face and his eyes are a normal brown.
Continuity mistake: In the pre-credits sequence when the gunman is shot by the police officer, he initially clutches a wound on his right side. When he is shown lying down, the bullet wound is higher up and on his left side.
Continuity mistake: When we see the Russian guy get shot and he falls out of his chair, he knocks the chessboard off the table. But when Jeffrey Spender shows his team the tape, the guy hits the board so that it spins around, instead of falling off completely. (00:02:40 - 00:07:55)
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