Revealing mistake: When Mulder is examining the residue on the mouth of the deceased man in The Beginning, the dead body's right eye twitches.
Continuity mistake: Mulder says that his sister “just disappeared from her bed one night” which is not true, because later visualizations of that moment show that Samantha was abducted while she and Mulder were playing a game and watching TV. (00:26:30)
Other mistake: When Mulder and Scully are first visiting Darlene Morris, there is a split-second shot of Mulder examining residue on his fingers that is edited in between Mulder and Scully ascending the steps to the porch and knocking on the door. It's as if the sequence was initially longer with Mulder discovering a suspicious substance before he and Scully knocked on the door that was not completely edited out. Note: this mistake may only appear on certain formats. At the time this mistake was originally posted, I spotted it on Netflix. However, it does not occur on my DVD, nor Hulu. (00:07:20)
Visible crew/equipment: In the scene at the very beginning of the episode, when the camera is going up the stairs, you can make out a man's reflection holding a camera on the stairs.
Continuity mistake: When Colonel Belt is going to bed after the press conference, the bottle on his side table moves between shots. (00:25:50)
Visible crew/equipment: In the scene where Scully is performing the autopsy on Micah Hoffman, you can see a shadow of someone moving across the wall behind her. (00:23:35)
Mind's Eye - S5-E16
Other mistake: When Marty is being transferred and 'sees' herself because the killer is watching her, she should have seen herself viewed through a wire fence, as the killer was standing behind one.
Continuity mistake: When Frohike plays the slot machine, the first position on the reel shows a single bar. After Byers spots Suzanne, the camera goes back to Frohike and the first position now is not a single bar. There wouldn't have been enough time between the shots for Frohike to have another pull of the machine. (00:10:15)
Continuity mistake: Mulder says that Scully was abducted and missing for four weeks. In "Duane Barry," the date stamp is given as August, then in "3," when Mulder returns to the X-Files office he turns the calendar all the way to November. Since Scully is returned the next episode after this, she must have been missing for at least 3 months, not 1. (00:06:20)
Factual error: The Beginning of the episode shows a baseball game taking place in Roswell, New Mexico. A ball smashes into a sahuaro cactus. The only place in the United States of America where sahuaros grow is in the Arizona desert. There are none in New Mexico.
Factual error: In this episode, Mulder says, "In 1996, a rock from Mars was found in Antarctica." The rock ALH84001 was found in 1984, and the announcement that it may contain life came in 1996. (00:17:55)
Revealing mistake: When Mulder finds the Japanese doctor dead on the floor of the train bathroom, the man's eyes are open. Just before the shot cuts to the girl and boy at the door, he closes his eyes.
War of the Coprophages - S3-E12
Factual error: In the scene where Mulder, the police officer and the doctor are in the doctor's room, the time on the clock reads 8:40. The doctor announces that he going to the bathroom. The scene cuts to him in the bathroom and then back to the doctor's office with Mulder and the police officer. Another cop comes in and says, "Come to the bathroom, something's happened." The clock still reads 8:40.
Soft Light - S2-E23
Continuity mistake: After the meeting with Dr. Davey, we cut to Mulder sitting in the train station trying to figure out what Dr. Banton was doing in the video. We see an overhead shot of the station, which shows a column in the far distance. Watch carefully: the shot never loses sight of the column, and you can see random passersby walk towards the column, but NO Scully. As the camera moves downwards to focus on Mulder in the foreground, Scully suddenly appears from behind the column, as if she had been walking towards it all this while. Obviously, she had been standing behind the column until her cue to come out. (00:19:45)
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)
Factual error: The alternate version of Scully is identified as an OSS agent, but the OSS did not exist in 1939. (00:34:35)
Continuity mistake: If you watch closely you can see that Mulder runs the key card through the door scanner the wrong way, scanning nothing but plastic. (00:25:40)
Continuity mistake: In this episode, both Mulder and Scully say that the last time they were in Oregon was 7 years ago. A previous episode this season dealt with the Millennium, so we know this episode took place in 2000. So seven years ago would be 1993, the year the show first aired. But in the Pilot episode, the corner of the screen reads their location in Oregon and March 7, 1992. 8 years ago. (00:08:20)
Miracle Man - S1-E18
Continuity mistake: In the establishing shot of the courthouse the subtitle reads "Kenwood County Courthouse" but you can read on the building that it is the "DeKalb County Courthouse". (00:15:15)
Mind's Eye - S5-E16
Continuity mistake: At The End of this episode when Mulder is talking to Marty through her jail cell, the position of their hands change. In one shot, Mulder's hand is covering hers, and in the next, each of their hands are gripping the cell bars. This goes back and forth a few times. (00:43:00)
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