Plot hole: On the phone, Scully asks for the report on her sister to be sent to the San Diego F.B.I field office (since she is visiting her brother and his wife and so is not in Washington), but the package is sent to her brother's home. Even if 'Danny,' whom she asks for the file, decided to be helpful and send it directly to her, her brother's address is not likely to be the one in her personal file, plus she didn't mention that that's where she'd be staying.
The X-Files (1993)
3 plot holes in season 5 - chronological order
Starring: Robert Patrick, David Duchovny, Annabeth Gish, Gillian Anderson, Mitch Pileggi
Factual error: Mulder refers to a Royal Navy vessel that sailed from Leeds. No large ship can sail from there - it is at least 50 miles from the coast.
More quotes from The X-Files
Trivia: Scully's father, Scully's older brother, and the man Mulder thought was his biological father were both named William. (The father who raised Mulder went by "Bill, " as did Scully's brother.) Mulder's actual biological father, Cancer Man, was played by William B Davis (who also goes by "Bill"). Scully and Mulder's son was also named William (before being adopted and having his name changed to Jackson).
Question: In a vast majority of the episodes, whenever Mulder and Scully investigate some mysterious or paranormal phenomenon, Mulder believes that some unknown force is responsible but Scully always has a rational explanation for what is happening. In other episodes, when Scully herself is caught up in something mysterious, she is the believer but Mulder is the skeptic. In those episodes, why would Mulder be skeptical about an unexplained phenomenon considering that he a was witness to his own sisters abduction and he saw many strange things that defied explanation while working for the F.B.I.?
Answer: A variety of reasons. Just because Scully saw something unusual does not mean that it was. Mulder always needs concrete proof before he'll believe there's some otherworldly explanation for unexplained phenomena. He's too experienced to take a novice's explanation as fact. It is also a plot by device by the writers to switch the tables on the characters to make it more interesting and to let viewers see another side of their relationship.
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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