Factual error: At the crime scene where Roland killed one of the professors by dunking his head in liquid nitrogen and dropped him on the floor, someone has drawn an outline of the dead prof's body and all the bits his head broke into when Roland dropped him. This outline-drawing doesn't happen in life because it interferes with the crime scene, it's a popular myth.
Factual error: Scully reads to Mulder from a book all about flukes (Trematodes). However, the information she is quoting is wrong. She states that flukes or flatworms have a "scolex" with hooks and suckers. These are actually the distinguishing characteristic of cestodes (tapeworms). Trematodes have no scolex and definitely no hooks. (00:17:30)
Continuity mistake: At The End, when Scully is trying to wipe sand and water from the moving tide away from a section of spacecraft, she stands up and the camera pans out; she is suddenly 3 feet away from the ship and several more away from the tide line.
Continuity mistake: After the part where the head Kindred woman tells Mulder and Scully "I asked you not to interfere", Mulder leads Scully away. From one camera angle, he is leading her away by the hand. In the same scene, but from a different camera angle, he has his arm around her. When we go back to the first camera angle, he is once again leading her away by the hand. (00:33:10)
Continuity mistake: In the mine with the medical records we see Samantha's file. In the season 1 episode "Conduit" we see the X-File Mulder opened on her. In the previous episode she is listed as Samantha T. Mulder and her birth date is 1/22/64. Here we see her name as Samantha Ann Mulder and her birth date as 11/21/65. (00:20:40)
Continuity mistake: Jeremiah Smith and Mulder are with the kids, and in the background, when CSM is looking through the window, Samantha's clone and the other kid disappear.
Continuity mistake: When Scully is reading report from Simmons' death, we can see that is has occured on the 7th of November, 1993; which means that whole episode takes place at the very beginning of November, but at the same time Scully and Mulder should be at Alaska (see episode "Ice"). (00:02:15)
The Sixth Extinction II: Amor Fati (3) - S7-E2
Continuity mistake: When Scully is talking to Skinner in Mulder's empty hospital room, her cross necklace is off to the left. Then, when she says, "Sir." it's almost centered. And no, this was not caused by her turning around a minute or so before she said it. (00:07:10)
Via Negativa - S8-E7
Continuity mistake: At The Beginning of the scene, there is only what seems to be a remote control on the left-hand side of the TV. Five seconds later, a couple of VHS tape cases appear where the remote control was before. (00:08:46)
Continuity mistake: Although the subtitle states 08:02 PM at the morgue, the clock in the room shows 08:40. (00:12:40)
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)
Plot hole: After less than 1 minute of investigation Scully found out that the photograph was bogus. It tells a lot about the "very best" specialists, mentioned by the Deep Throat later on, who had prepared the photo. (00:19:10)
Plot hole: Mulder is pulled from the escape hole previously dug by the hybrid aliens to escape the train car. When they pull him out they show alien bodies remaining in the hole. Mulder never revisits the train car despite knowing there's a high probability of finding hard evidence, in this case some actual bodies. There's no way Mulder would just assume there's no evidence remaining there and not go have a look for himself. Same goes for Cancerman who thought he had destroyed the evidence.
Continuity mistake: The lamp and the bottle behind FBI official Scott Blevins near the start change places between shots. (00:03:12 - 00:05:00)
Factual error: The subtitles state an office in Maryland, but in front of the building, we can see California's flag. (00:06:37)
Continuity mistake: The remote control, close to the TV, changes position in between shots near the start. (00:05:03 - 00:05:29)
Continuity mistake: Near The End of the episode, Mulder is reviewing black-and-white photos of The Jersey Devil. A wedding ring is visible on The Jersey Devil's left hand in the photo. Earlier in the episode, she is not wearing the ring.
Factual error: A number of episodes show trolleybuses operating in American cities that do not use them (including Washington). Vancouver, where the series was filmed, however, does use them.
Visible crew/equipment: When the tiger is on the loose it prowls around a building site and there is a shot where you can see the animal trainer calling the tiger right to him. (00:23:56)
Born Again - S1-E22
Continuity mistake: When Felder is being strangled to death by his scarf getting trapped in the bus door, pay attention to the bus driver throughout the sequence. He is a young black guy for most of the sequence however there is one shot from the front of the bus were you can see he has suddenly changed to a white man. (00:21:53)
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