Plot hole: After Exley has gotten up after being hit by the ball, Dales notices green alien blood inside the glove where the back of Exley's head was resting. However, Exley was hit in the face, not the back of the head; not only was there no bleeding face wound while he was on the ground, but the glove was clean when Exley first gets up.
Plot hole: When Arthur looks closely at the green alien blood on the baseball glove, he has no reaction to it, despite the continuous pattern in the show about the blood being incredibly toxic to humans, even from a distance. It should have badly hurt his eyes at the least.
Other mistake: When Mulder is on his knees in the cafeteria talking to the gunman, there are several shots where you can see the sides of his jacket hanging wide open because of his raised arms, which would make the gun on his belt easily visible to the gunman as he talks to him, but he somehow doesn't see it until he goes to take Mulder's phone.
Visible crew/equipment: When Ben Drake is walking in front of the paintings in his office, for a short moment one can see the camera setup and the cameraman reflected off the first painting. (00:01:40)
Continuity mistake: During the conversation with Mulder, in the front shot the Deep Throat tilts his head to the left while in the back shot his head is tilted to the right. (00:26:10)
Continuity mistake: When Scully enters her apartment, the blinds are up and there is quite a lot of light in the room. However, when the flashback with Mulder ends, during which Scully was supposedly standing still, the shades are rolled down and there is much less light in the room. (00:20:30)
Empedocles - S8-E17
Continuity mistake: When the fiery figure comes up to Jeb, he is standing alone on the street, however in the previous and following take he stands in the crowd surrounded by other people. (00:02:15)
Continuity mistake: In the opening scene, when the guy is calling from the booth, he is standing either on the left or right side of it, depending on the shot. (00:00:40)
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.
