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.
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)
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