Continuity mistake: Just as Mulder and Scully are entering the interrogation room to question Lauren for the second time, Mulder is holding a thin stack of paper, folded in half in his right hand. In one shot, these are folded horizontally. In the immediate next shot, they are now folded vertically. (00:34:20)
Clyde Bruckman's Final Repose - S3-E4
Revealing mistake: When Mulder and Scully discover Clyde's dead body, if you look closely you can see Clyde's left eye twitching. (00:43:05)
Continuity mistake: Agent Frank Burst screams "Stop!", but in the previous shot the police car was already stopped, although deputy Scott Kerber has just pushed the accelerator. (00:03:30)
Continuity mistake: After the crash Mulder rests his head on the passenger dashboard, however in the previous shot filmed from the outside he keeps it on the headrest. (00:08:30)
Continuity mistake: While hugging detective White, in the first shot Mulder's tie covers his shirt's collar, but in the next shots the tie is hidden under the collar. (00:26:10)
War of the Coprophages - S3-E12
Continuity mistake: The bug exterminator squeezes his throat with either left or right hand depending on the shot. (00:02:25)
Revelations - S3-E11
Continuity mistake: When filmed from the inside of the basket, the openings in the basket structure are big enough to put a finger into it, while in the outside shot the structure is compact and dense. (00:21:00)
Visible crew/equipment: As the camera flies over the train, in the upper right corner of the screen there is some equipment and umbrella visible that are not likely to just be in the middle of nowhere - probably filming equipment. In the next shot they are gone. (00:31:05)
Revealing mistake: The guy who is jumping to the water is definitely not Mulder. It is a stunt. (00:21:20)
Continuity mistake: Mulder jumps down by the fence in two configurations: one when he is filmed with a closeup (left side), and the other while he is filmed from the distance just a moment after (right side). (00:08:15)
Other mistake: It seems that the first round fired by the hit squad destroys the camera or its power supply unit, because the satellite transmission is interrupted exactly at the moment the squad enters the train car. However, the members of the squad firstly shoot in the glass and then at the doctors. (00:06:25)
Continuity mistake: Near the start, the train on the track adjacent to the train car's track is either moving or not, depending on the shot. (00:01:05)
Plot hole: The guy who was standing at the back of the train car was somehow able to move to the front of it. This was impossible because the train car was sealed and no unauthorized person could enter it. (00:00:50)
Other mistake: There is too much light on the ceiling for the tiny hole Amy accidentally discovers on the wall. In one shot it is plain to see that there are other light sources. (00:20:00)
Continuity mistake: Ellen stays by the door looking to the right from it, but in the next shot she looks straight at Mr Incanto. (00:33:55)
Revealing mistake: When the car hits the tree, one can notice that there's a stunt sitting behind the wheel instead of the warden. (00:42:05)
Factual error: Mulder tells Scully that he is trying 27828 and it is not working. It is not surprising that it is not working, because the Napier constant is not 27828, it is 271828. Plus they somehow they know how many digits from this constant should be entered on the keyboards. (00:15:55)
Other mistake: The heavy rain falls and bangs on the greenhouse roof, although Mulder and Scully are completely dry, even though they carry no umbrella with them. (00:10:20)
Soft Light - S2-E23
Factual error: Dr Banton's shadow devours the second policeman, however Banton cannot cast a shadow in that direction. (00:11:35)
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