Continuity mistake: When Scully arrives to investigate the kid who was crushed by the bleachers the time stamp says 5:10AM. It seems strange that the investigation would start the next morning, unless the high school holds basketball practice at 3:00 in the morning. (00:16:35)
Continuity mistake: Mulder recalls to Scully that he saw Krycek being pulled out of the car and then saw the bright flash, but he only came to just in time to see the flash. (00:08:50 - 00:12:00)
Continuity mistake: In the pre-credits sequence when the gunman is shot by the police officer, he initially clutches a wound on his right side. When he is shown lying down, the bullet wound is higher up and on his left side.
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)
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.
Other mistake: After AD Skinner is finished being interviewed by the police, Mulder asks him about why he would employ the services of a prostitute. Skinner looks at him in shock and Mulder says "You didn't know she was a prostitute did you?" I find it hard to believe that at no point in the interview did the police not mention to Skinner the dead woman he woke up next to, after spending the night with her, was a prostitute.
Continuity mistake: Pusher loads the revolver with one bullet, leaving five chambers empty. When Mulder picks it up and points it at Pusher, the bullet can be seen in the cylinder, just to the right of the gun barrel. Later, when Mulder begins to slowly pull the trigger for the third time (aiming at Scully), we see the cylinder turn to Mulder's left. Problem is, with the bullet situated as it was when Mulder picked it up, the bullet would have moved to the barrel and been fired the first time he pulled the trigger, killing Pusher. Instead, it fires on the third pull.
Plot hole: When Mulder and Scully are going to the town/city where the disappearances took place Scully says they should stop so she can walk the dog. Mulder says OK because he has to ask for directions yet the next scene we see is Mulder and Scully interviewing Dr. Faraday. How did they find him if they didn't know where they were?. And after that we see them at a store where they do ask for directions. (00:08:30)
Factual error: At The Beginning of the scene, XO Johanson is looking through the periscope. However, it is nonsense, because the submarine was in silent running, and the Japanese destroyer was circling it, so the sub must have cruised in deep submersion. The water depth there was approx. 270 meters, as the French salvage team claims at The Beginning of the episode. There is rarely any significant light beyond 200 meters. Looking through the periscope in these conditions would be completely useless. (00:32:25)
Revealing mistake: At the very beginning of the scene when the bomb is shown, in the lower part of the screen a moving red spot appears which probably comes from the reflection of the bomb's red diode in the camera. (00:36:50)
Factual error: The crew are supposed to be French. However at The Beginning of the episode we can hear them talking in French with a Canadian accent.
Revelations - S3-E11
Continuity mistake: Kevin's mother uses her car to hit the 'devil' and shatters the bottom right of the windscreen. The following shots, including the crash into the ditch, show the car with the windscreen undamaged. (00:28:59 - 00:29:22)
Continuity mistake: During the very beginning of the episode when the cop and researcher are talking on the shore they go from facing each other to the cop facing the lake and having to turn his head to talk to the researcher between shots. (00:00:30)
Other mistake: When Mulder and X are standing outside the Mulders' summer house, we hear that it is raining, but there is no sign of rain on neither of them. (00:17:50)
Visible crew/equipment: After Lieutenant Colonel Stans (who has severe burns all over his body) kills Leonard Trimble, he turns to the camera, where his bathrobe is not fully covering the burn mask he is wearing, exposing a part of his shoulder and the edge of the mask. (00:42:35)
Visible crew/equipment: At the silo in North Dakota, the camera pans around the vehicle after Mulder and Scully arrive. The boom mic is reflected in the passenger doors.
Continuity mistake: When Mulder tells Krycek to go to the bathroom and clean off, in the front shot Krycek holds his right hand raised, while in the back shot his right hand is lowered. (00:42:10)
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.
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