Continuity mistake: When Mulder experiences his near-death trance state his body is lying, apparently lifeless, in a star spangled sky. As the camera tracks in on him the toes on his right foot twitch, just after Deep Throat begins to speak. The foliage covering his chest also changes position between shots. In the wide shot he is covered up to the armpits. But the first close up shows his chest is exposed. Then in later close ups it is covered again. (00:14:25)
Plot hole: Mulder is pulled from the escape hole previously dug by the hybrid aliens to escape the train car. When they pull him out they show alien bodies remaining in the hole. Mulder never revisits the train car despite knowing there's a high probability of finding hard evidence, in this case some actual bodies. There's no way Mulder would just assume there's no evidence remaining there and not go have a look for himself. Same goes for Cancerman who thought he had destroyed the evidence.
Factual error: In the footage's right-hand side, we can see the Church of the Covenant's facade, which is located at East 42nd St. New York. However, the subtitle erroneously states 46th St. (00:09:40)
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)
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)
Visible crew/equipment: When Mulder and Scully enter the abandoned mine through a doorway, the viewer can see at right in the distance a number of people sitting on a wall, and one crouching in front of the wall with what looks like a dog. They are sitting still, but there is still movement there. (00:16:00)
Continuity mistake: In the mine with the medical records we see Samantha's file. In the season 1 episode "Conduit" we see the X-File Mulder opened on her. In the previous episode she is listed as Samantha T. Mulder and her birth date is 1/22/64. Here we see her name as Samantha Ann Mulder and her birth date as 11/21/65. (00:20:40)
Factual error: Skinner says that he could not print the file. However, Scully somehow must have been able to print it in order to give a hard copy to Albert Holsteen for his translation. (00:26:35)
Continuity mistake: The car where the guy is killed is a 1970 Ford LTD convertible in front but a 1969 Ford LTD from the rear.
Clyde Bruckman's Final Repose - S3-E4
Visible crew/equipment: When the agent says "I'm Kline, this is Havez" the boom mic is by the light on the ceiling. (00:04:15)
Clyde Bruckman's Final Repose - S3-E4
Continuity mistake: Clyde Bruckman commits suicide by placing a plastic bag over his head until he asphyxiates. However, when Mulder and Scully first discover him you can see in the shot just before Scully holds his hands that there is no plastic bag around his head (may only be visible in widescreen format). (00:42:55)
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)
Clyde Bruckman's Final Repose - S3-E4
Character mistake: Clyde Bruckman says that the Big Bopper won a coin toss that put him on the plane that crashed and killed him along with Buddy Holly and Ritchie Valens. The person who actually won the coin toss was Ritchie Valens.
Audio problem: J.T. Walsh is talking to Mulder and Scully about how smart the inmate was. During this sequence, one of the scenes has very poor audio sync. J.T. Is talking but his mouth doesn't match what he is saying. (00:07:25)
Continuity mistake: Later in the episode a man bangs on an air conditioner to try and stop it from making noise. In the first scene you can tell air is moving because the streamers are moving. After he bangs on the unit the streamers stop moving. The air conditioner is still on. (00:32:30)
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)
Continuity mistake: During the autopsy, Scully says that the date is August 29. The two previous episodes were set in September. (00:09:50)
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)
Continuity mistake: The drawing image of the killer loads twice on the computer. You can see it start to load in the first shot which is closer. In the very next shot it loads from nothing again.
Visible crew/equipment: When the apartment owner comes over to the killer's apartment, she puts an envelope over near others. Right as she notices the flies, the camera tracks to the left and back. You can see its shadow cast on the wall to the left.
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