Factual error: According to the NASA space shuttle launch countdown procedure, the close-out crew retreats to fallback area in the "T-3 hours and counting" phase. The members of the crew are the last persons who leave the launch pad at least 20 minutes before liftoff. However, during the close-up take of the main engines, when the ground control says "All systems go for APU start", we can see two members of the ground personnel in orange suits near the engines.
Continuity mistake: When Scully walks into Mulder's office, she stops in the position with the "I want to believe" poster in the background, then she takes a couple of steps to make acquaintance with Mulder, and she finds herself again in the position with the poster in the background.
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.
Continuity mistake: Later in the episode a man bangs on an air conditioner to try and stop it from making noise. In the first scene you can tell air is moving because the streamers are moving. After he bangs on the unit the streamers stop moving. The air conditioner is still on.