Factual error: The Arecibo Radio Telescope is abandoned when Mulder goes there. However, after SETI was cancelled, the telescope was still used for other things. (00:16:50)
Continuity mistake: When Mulder is in the tower and Scully has just found him the sweat patches on his shirt change in between shots. (00:40:00)
Continuity mistake: When Fox Mulder is having the flashback when Samantha was abducted, he looks at the doorknob, in the close-up he is still looking at the doorknob but it has changed colour.
Plot hole: At his arrival at the Arecibo observatory, Mulder crushes the padlock on the door leading to the control building, and then he finds the native man, Jorge, in the toilet, who hid himself in the building. There's no way Jorge could enter the building and also lock himself in there with the padlock. (00:17:45)
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