Revealing mistake: At The Beginning of the episode we see Duane being abducted and he begins to scream. Look at the "alien" on the left of the screen near to the top of the bed and you will see him move his head revealing where the suit ends and neck/head begins. (00:02:12)
Revealing mistake: When Scully makes a purchase at the grocery store, shortly before she scans the metal fragment, the clerk gives her the total of the sale, however, shortly after the camera captures the register, which displays ‘no sale'. (00:41:30)
Revealing mistake: The answering machine at The End appears to not be plugged into any phone line. The shot shows the phone jacks on the right side of the machine are empty. In order for an answering machine to work at least one of those ports would need to be hooked to the phone.
Other mistake: An agent and Scully analyze the fragment taken out from Duane Berry's body. The agent draws Scully's attention to "small markings", which are half a monitor size, and Scully naively asks where they are. (00:39:00)
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