Continuity mistake: When Mulder breaks into the boat, the door shuts, but in the next shot it's wide open. Shot after that, it's closed again.
Continuity mistake: If you watch closely you can see that Mulder runs the key card through the door scanner the wrong way, scanning nothing but plastic. (00:25:40)
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: 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)
Revealing mistake: When Mulder finds the Japanese doctor dead on the floor of the train bathroom, the man's eyes are open. Just before the shot cuts to the girl and boy at the door, he closes his eyes.
Factual error: In the opening scene it says it takes place in West Virginia, as the Army unit executes the hybrids, you can see their unit patch on their left shoulder. The patch is a diamond shape with a sunburst in the middle, this is the patch of the 40th Infantry Division of the California Army National Guard.
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)
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)
Revelations - S3-E11
Factual error: After the agents meet with Kevin's father in the mental institute, Scully lists the medication that he is on: haloperidol, loxapine, and chlorpromazine make sense, but the fourth medication - LARGACTIL - is in error. Not only is it a brand-name of chlorpromazine, but it is not available in the USA, it is a CANADIAN drug. (00:36:10)
Revelations - S3-E11
Visible crew/equipment: The camera and its operator are visible in a piece of metal on the back of the ambulance, when the mother is taken away after the accident.
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)
War of the Coprophages - S3-E12
Factual error: In the scene where Mulder, the police officer and the doctor are in the doctor's room, the time on the clock reads 8:40. The doctor announces that he going to the bathroom. The scene cuts to him in the bathroom and then back to the doctor's office with Mulder and the police officer. Another cop comes in and says, "Come to the bathroom, something's happened." The clock still reads 8:40.
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)
Visible crew/equipment: When Scully says "This is rumor panic" you see the camera shadow following her on the lower left side of screen. (00:18:20)
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)
Continuity mistake: The glass in the picture of Ryan Reynolds cracks as the casket is starting to catch fire. In one shot, which is wider, the glass has fixed itself. Cut to a closeup, the glass is broken again.
Continuity mistake: When Scully and Mulder first visit John Mostow he says that he drew all the pictures of Gargoyles, which would have been a pretty good act considering he was in a strait jacket and would not have been allowed to have paper and drawing materials anyway. (00:07:30)
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)
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: When Skinner walks into the cafe (the time he gets shot) another man is just walking out, leaving a table with a used glass and coffee cup. The waitress is in the back, getting Skinner a cup of coffee (she couldn't have cleaned the other table yet), but when we look over Skinner's shoulder you can see that the other table is cleared and has a clean coffee cup (turned upside down) on it.
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