Revealing mistake: While the computer is being infected with the virus, Peterson turns away from the screen to face Scully. Two seconds later, after the shot of Scully, the same shot is shown again but in reverse so that Peterson turns back to the screen. It's more obvious if you look at the weird way his eyes blink in the reversed shot. (00:39:50 - 00:41:32)
Audio problem: When Jerry uses the elevator, the voice of the computer reads out the floors as "twenty-third floor, fourth floor, fifth floor" etc, missing out the "twenty-" prefix until the 29th floor. The DVD subtitles list these numbers with their prefix, so this was not intentional. (00:21:10)
Visible crew/equipment: When Brad is showing Mulder and Scully the video tape in his house, you can see the crew reflected off the TV screen. (00:12:50)
Other mistake: Near The Beginning, we see security camera footage from a computer watching Drake type a letter about cancelling the COS project. The footage is too low to be shot by the security camera. It's the regular camera that continues the scene since there is a cut to it from the monitor (and the shot pans to the right before Drake is killed). Many TV shows and movies forget to line up the POV shots from security cameras, using the real footage instead.
Visible crew/equipment: When Ben Drake is walking in front of the paintings in his office, for a short moment one can see the camera setup and the cameraman reflected off the first painting. (00:01:40)
Continuity mistake: During the conversation with Mulder, in the front shot the Deep Throat tilts his head to the left while in the back shot his head is tilted to the right. (00:26:10)
Continuity mistake: When we watch Scully typing from behind, the text she types is ahead of the text we saw at a distance in the previous shot. (00:15:15)
Visible crew/equipment: Mulder is talking to the computer programmer in the prison. The shot starts on the bars and pulls back. A significant shadow caused by the camera is visible on the right side of the frame.
Continuity mistake: When Scully gets out of the car, it is parked much closer to the curb than in the previous shot. (00:30:35)
Other mistake: It's incomprehensible why such an intelligent COS has to print out the stolen data on Scully’s monitor, risking being exposed. (00:15:40)
Other mistake: When Jerry Lamana goes up in the elevator in the Eurisko building, the "thirteen floor" message is missing. (00:20:55)
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