Continuity mistake: When the prostitute, Holly MacClaine, is first murdered, we see her face up. The next morning, when the police are at the crime scene, we see her face down.
Continuity mistake: General Callahan tells Mulder that the man he saw in his office said his name, but all he said was, "Your time has come, killer". (00:13:10 - 00:17:25)
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)
Deliberate mistake: It's completely impossible that the sound of the tape(that sounds like "Fox Maytrink") is in fact "Your time has come,Killer".
Continuity mistake: General Callahan, who is referred to as General Callahan throughout the episode by Mulder, gets called "Lieutenant" Callahan in the last scenes in the steam-room, while lying on the floor.
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)
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)
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)
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: 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)
Revealing mistake: The guy who is jumping to the water is definitely not Mulder. It is a stunt. (00:21:20)
Continuity mistake: When Senator Richard Matheson tells Mulder about the four Japanese Nationals had been murdered, he says that the murders had occurred several weeks ago. But when Mulder brings Scully up to speed a scene or two later, he tells her that someone must have been able to identify the four doctors who were performing the autopsy because they were murdered YESTERDAY. (00:30:05 - 00:33:10)
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)
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