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.
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