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)