Continuity mistake: In The Beginning, when the Bounty Hunter gets out of his car, Jeremiah Smith says nothing. However, in the same scene at 42:08 in the "Talitha Cumi" episode, Jeremiah says "He is here to kill me." (00:00:05)
Continuity mistake: Scully tapes an X in the window,that X changes shape when Scully is talking to Mr. X and before Mr.X dies when he checks on the apartment.
Continuity mistake: Jeremiah Smith and Mulder are with the kids, and in the background, when CSM is looking through the window, Samantha's clone and the other kid disappear.
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