Factual error: In the opening scene it says it takes place in West Virginia, as the Army unit executes the hybrids, you can see their unit patch on their left shoulder. The patch is a diamond shape with a sunburst in the middle, this is the patch of the 40th Infantry Division of the California Army National Guard.
Musings of a Cigarette-Smoking Man - S4-E7
Revealing mistake: As the smoking man sits on a bench after finding out his story was rewritten, there are mountains visible in the background. Atop one of the buildings in the background is a Canadian flag waving in the wind. This show was shot in Vancouver, but is set in Washington D.C. There are no tall mountains that close to D.C.
Continuity mistake: When Mulder and Scully are arguing outside the hospital, after meeting Billy and Peggy, there is a woman in a red coat, behind Scully, who gets out of her car and then vanishes between shots. (00:19:30)
Deep Throat - S1-E2
Other mistake: When Scully and Mulder are pulled over by the government agents, one agent takes and unloads Scully's gun. When he removes the magazine you can see it has only one bullet in it, as this model of magazine has cutaway sides to show the amount of bullets in them. (00:26:47)
Factual error: The episode is supposed to take place in Traverse City, Michigan, United States. Mountains are visible in the sequence when Mulder is chasing after the killer on foot. The show was shot in Vancouver, British Columbia.
Deep Throat - S1-E2
Continuity mistake: When Scully is holding the guy's airbase security ID badge it changes between shots.
Plot hole: The bugs are related to a type of mite, and when they are shown under a microscope they look like a glowing lice without wings. The problem is they are swarming in the air so they have to be able to fly - no way to do that without wings.
Factual error: When Byers asks Langly to try under active cases to find Holly Modeski in the FBI database, Langly only presses two or three keys on a keyboard, which is obviously not enough to enter "Holly Modesky" to the search engine. (00:19:40)
Factual error: When two unidentified men who approached Susanne Modeski in the warehouse take out their handguns, they have regular pistols. However, when they start to shoot, continuous fire is heard that could only be produced by an automatic weapon. (00:28:40)
Suggested correction: Fully automatic pistols exist, such as the Glock 18.
Continuity mistake: The glass in the picture of Ryan Reynolds cracks as the casket is starting to catch fire. In one shot, which is wider, the glass has fixed itself. Cut to a closeup, the glass is broken again.
Revelations - S3-E11
Visible crew/equipment: The camera and its operator are visible in a piece of metal on the back of the ambulance, when the mother is taken away after the accident.
Nothing Important Happened Today II (2) - S9-E2
Factual error: Deputy Director Alvin Kersh tells Agent Doggett a story about King George III, who, on July 4th, 1776, the same day the American colonies declared their independence, allegedly made an entry in his diary: "Nothing important happened today." However, according to Arnold Hunt, curator at the British Library, King George III never kept a diary. (00:37:15)
Plot hole: Josh Exley's 'real' face shouldn't be visible as a reflection on the window. It's not an illusion that he creates to fool people, whereby his real self could theoretically be seen in a reflective surface, but a complete physical change, as we've seen in many episodes of the X-files regarding the shape-changing abilities of the aliens. What his face appears to be while altered is essentially what it is, and the reflection should show as much.
Other mistake: When Jerry Lamana goes up in the elevator in the Eurisko building, the "thirteen floor" message is missing. (00:20:55)
Continuity mistake: While Mulder and Scully are in the woods, in some shots it is raining, while in others there is no sign of the rain. (00:21:00 - 00:23:15)
Other mistake: Padget hands over one page of his book to his imagined character who is invisible to anyone else except him. Therefore, the page should hover in the air for an external observer. However, Scully watches his apartment on a monitor and notices nothing strange. (00:38:05)
Plot hole: Big Mike was attacked by the creature, because his bulb was broken just for a couple of seconds. It would mean that even if something like this happened to somebody else by accident, this person would also be killed by the creature. That would drastically increase the kill rate in the community. (00:16:15)
Suggested correction: That was the whole point of the creature, to enforce the HOA rules so that no violations occurred, even by accident. Although prior to the attack, Gene Gogolak describes Big Mike as a weak link that had to be dealt with, so the bulb was just an excuse to attack him.
Continuity mistake: At The Beginning of the scene in his office, in the front shot Skinner wipes his glasses in his hands, but in the following back shot he's wearing them. (00:12:25)
Character mistake: Pusher says that he read in Scully's files that she had shot Mulder, although after Pusher's visit in the Computer Records Office Skinner says that Pusher checked only Mulder's files. (00:40:15)
Factual error: When Mulder is walking out of the cabin in Spender's uniform, the soldiers try to stop him. This is impossible since he is an officer (a lieutenant judging from the shoulder-straps) and they are privates, so they cannot give him orders. The only thing they can do in this situation is to salute him. (00:08:40)
