Plot hole: After less than 1 minute of investigation Scully found out that the photograph was bogus. It tells a lot about the "very best" specialists, mentioned by the Deep Throat later on, who had prepared the photo. (00:19:10)
Other mistake: Mulder pulls in to park in front of a red car. The front plate on both Mulder's and the red car is the same: 5S2 706. (00:27:37)
Miracle Man - S1-E18
Continuity mistake: The young Samuel stretches his palms upwards, while in the next shot the boy holds them straight. (00:01:00)
Miracle Man - S1-E18
Continuity mistake: In the establishing shot of the courthouse the subtitle reads "Kenwood County Courthouse" but you can read on the building that it is the "DeKalb County Courthouse". (00:15:15)
Miracle Man - S1-E18
Character mistake: Scully says "She is dead" instead of performing cardiac massage, as any other doctor would do. (00:25:45)
Continuity mistake: When Mulder and Scully talk about the piece of skin while driving to the reservation, one can see that there are green trees from the Mulder's side of the road, but when the shot is taken from the outside of the car, there are only grey bushes and landscape devoid of nearby trees on both sides of the road. (00:07:00)
Continuity mistake: At The End of the episode, when Lyle is transforming in the bathroom, we see his hand perfectly shred a shower curtain, however in the next shot we see his hands and they are still fully human. There's no way he could have done that. (00:38:44)
Continuity mistake: When they find the felled ancient tree, the stump that Mulder clambers up onto to investigate the growth rings has a distinctive crack at the center and the growth rings are irregular in shape. However the stump that we get a close up of has no crack and regular circular rings. (00:18:20)
Continuity mistake: When they find the cocoon, the body inside is completely different in appearance from one shot to the next shot of it.
Plot hole: The bugs are related to a type of mite, and when they are shown under a microscope they look like a glowing lice without wings. The problem is they are swarming in the air so they have to be able to fly - no way to do that without wings.
Continuity mistake: When Tooms walks out of the courtroom, the doctor and the old lady who were sitting in The Beginning of the corridor are missing. (00:11:45)
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.
Born Again - S1-E22
Continuity mistake: When Scully is doing the exam on the dead guy on table, he blinks and breathes. (00:12:05)
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)
Factual error: At the crime scene where Roland killed one of the professors by dunking his head in liquid nitrogen and dropped him on the floor, someone has drawn an outline of the dead prof's body and all the bits his head broke into when Roland dropped him. This outline-drawing doesn't happen in life because it interferes with the crime scene, it's a popular myth.
Other mistake: Deep Throat says that Mulder and Scully are standing in the very room, where "the first human-alien hybrid was created." However, only in the "Patient X" episode, are we told that it is Cassandra who has just become the first successful human-alien hybrid. (00:28:00)
Continuity mistake: When the Smoking Man brings the alien fetus to the Pentagon storage facility, he places it on the second rack, then in the next shot he walks away from the rack situated in the middle of the corridor. (00:42:55)
Visible crew/equipment: After talking to the scientist about his car, Mulder and Scully are talking in front of a door. In the glass of the door is a reflection of a third person.
Factual error: The Arecibo Radio Telescope is abandoned when Mulder goes there. However, after SETI was cancelled, the telescope was still used for other things. (00:16:50)
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