Visible crew/equipment: Mulder talks to the man from NICAP on the other side of the fence. When the shot is looking at the man, film lights are visible reflected in his glasses. Since he is looking at Mulder, there should be lights on Mulder's side, but there are none.
Visible crew/equipment: Mulder is talking to the computer programmer in the prison. The shot starts on the bars and pulls back. A significant shadow caused by the camera is visible on the right side of the frame.
Audio problem: The man changing the flat tire in The Beginning of the episode drops his flashlight. He says "dang it" but his mouth doesn't move.
Deep Throat - S1-E2
Revealing mistake: Mulder pulls away from the hotel after telling Scully he is going to shower and then they'll leave. The tire marks from previous takes are visible on the pavement.
Factual error: In the opening sequence, we see a nuclear attack submarine beneath the ice in the Arctic Ocean. When the captain orders the ship to surface, one of the crewmen mutters, "Surface to what? We're under 32 feet of glacial ice!" Except that they're not under "glacial ice," they're under Arctic sea ice, which ranges from about 6 feet thick in the summer to about 15 feet thick in the winter.
Other mistake: In order to leave such bloody footprints, CSM must have stepped into the puddle of blood. It is impossible because the guy shot by CSM could not bleed so much blood in such short time, not mentioning that CSM must have intentionally stepped into it. (00:05:20)
Continuity mistake: The chessboard was knocked down by the falling Russian, however in the next shot it is still on the table. (00:02:55)
Continuity mistake: When Dara walks toward the angel, there is only one car, parked on the right side of the street, but when her father approaches her, there is another car parked on the opposite side of the street. (00:02:50)
Unrequited - S4-E16
Continuity mistake: When Scully and Mulder run away from the dogs, the gate is fully open, while in the previous and next shot only the door is open. Plus their car standing in front of the gate is missing. (00:09:30)
Continuity mistake: The wedding ring Ariel is holding in her outstretched hand is either vertically protruding from the palm of her hand or is hidden inside of it, depending on the shot. (00:40:25)
Continuity mistake: While Mulder's waiting for Langly and Frohike to unlock the exit door, Gray-Haired Man keeps shooting at the glass door, and the increasing bullet damage on the glass doesn't stay consistent as more damage occurs, and changes between the closeups and wideshots.
Continuity mistake: When Mulder and Byers find Scully in Penny's room, there is a black stripe on the ceiling of the corridor, while in the scene when Scully is leaving the room there is no stripe there. (00:36:50)
Never Again - S4-E13
Continuity mistake: In the front shot Scully holds the photo with 2 fingers (thumb and index), while in the back shot she uses three fingers (thumb, index, and middle). (00:24:55)
Continuity mistake: When Mulder is talking to Dana's mom about finding her cross (necklace) in the trunk, Scully's mom says that she gave it to her on her 15th birthday, but in Season 5 in Christmas Carol, Scully has a flashback to receiving it at Christmas. (00:41:40 - 00:43:55)
Mind's Eye - S5-E16
Continuity mistake: While talking through the jail glass, Marty's face is generally directed straight toward Mulder's face when reflected in the glass, but her head is twisted to the right when filmed from Mulder's side. (00:34:40)
Mind's Eye - S5-E16
Visible crew/equipment: During the scene of Marty's interrogation there is some dark blue element behind Mulder when he is reflected in the mirror. However, in the frontal scene there is just a plain wall behind him. (00:24:00)
Mind's Eye - S5-E16
Continuity mistake: When the policeman passes the phone over to Marty, in the first shot from behind she holds it with two hands, while in the next frontal shot she grabs it with her left hand and then with the right hand. (00:13:20)
Mind's Eye - S5-E16
Other mistake: Since the apartment was supposedly "turned inside out and upside down, " as Detective Pennock claims, it would be practically impossible that such an obvious place as the shaving blades container not be dug up thoroughly by the police. (00:12:15)
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)
Nothing Important Happened Today (1) - S9-E1
Continuity mistake: During the previous episode, Skinner receives a nasty gash on his head courtesy of Billy Miles. This episode takes place 48 hours later and there is no indication whatsoever that Skinner received such an injury (the wound is visible once again in the next episode). (00:15:35)
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