Continuity mistake: During Colonel Belt's funeral, there are saluting soldiers standing behind Michelle in some shots, while in others they are not there. (00:43:45)
Continuity mistake: When Skinner is stopping Mulder from hitting Krycek, in the back shot Mulder keeps his hand on Skinner's neck, while in the front shot he keeps his hand somewhere else. (00:31:50)
All things - S7-E17
Other mistake: The surname on the envelope is "Szczesny" (which is of Polish origin and means "Lucky"), so its pronunciation should be something like "shtcheznhy." However, in the subtitles the surname is written as "Szezesny" and pronounced by Scully accordingly. (00:06:30)
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.
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)