Revealing mistake: During the opening funeral scene if you look closely you can see the dead girl breathe. (00:02:28)
Born Again - S1-E22
Continuity mistake: When Felder is being strangled to death by his scarf getting trapped in the bus door, pay attention to the bus driver throughout the sequence. He is a young black guy for most of the sequence however there is one shot from the front of the bus were you can see he has suddenly changed to a white man. (00:21:53)
Visible crew/equipment: When female Marty gets out of the car for the police officer if you look at the left side of the screen you can see the male Marty actor stood there wearing matching clothing and watching the filming. (00:36:33)
Other mistake: At The Beginning when Mulder and Scully leave the room and walk across the FBI office you can see and hear the camera get knocked to the left by something (it was probably the filing cabinet that they walk past a second later). (00:05:19)
Revealing mistake: At The Beginning of the episode Darlene burns her hand trying to open the door, she then puts on an oven mitt and opens the door. If you look closely though she still uses her other naked hand as well as the covered hand to open the door and her naked hand is completely unhurt.
Revealing mistake: After Scully handcuffs Tooms to the bathtub there is a close up of his face and you can see the edge of his contact lens. (00:39:07)
Audio problem: Scully asks the deputy if the vests are necessary and he replies in the same scene. His mouth is way off from his reply. It's likely this is because the show was shown on 4:3 aspect ratio televisions at the time, and he would simply not be visible. Because the show was shot in 16:9, he is very much visible on modern televisions and the mistake is incredibly obvious.
Factual error: The package Scully receives lists her city, state, and zip code as Bethesda, Maryland 20880. While that is an actual zip code in Maryland, it is for Washington Grove, not Bethesda.
Nothing Important Happened Today (1) - S9-E1
Character mistake: When Agent Dogget is eating breakfast, he listens to the information in TV news about "the body of 38-year-old Carl Wormus." However, the obituary which Agent Reyes is reading later says that "Carl Wormus was found dead at the age of 45." (00:07:30)
Factual error: In the opening scene it says it takes place in West Virginia, as the Army unit executes the hybrids, you can see their unit patch on their left shoulder. The patch is a diamond shape with a sunburst in the middle, this is the patch of the 40th Infantry Division of the California Army National Guard.
Musings of a Cigarette-Smoking Man - S4-E7
Revealing mistake: As the smoking man sits on a bench after finding out his story was rewritten, there are mountains visible in the background. Atop one of the buildings in the background is a Canadian flag waving in the wind. This show was shot in Vancouver, but is set in Washington D.C. There are no tall mountains that close to D.C.
Deep Throat - S1-E2
Other mistake: When Scully and Mulder are pulled over by the government agents, one agent takes and unloads Scully's gun. When he removes the magazine you can see it has only one bullet in it, as this model of magazine has cutaway sides to show the amount of bullets in them. (00:26:47)
Factual error: The episode is supposed to take place in Traverse City, Michigan, United States. Mountains are visible in the sequence when Mulder is chasing after the killer on foot. The show was shot in Vancouver, British Columbia.
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