Other mistake: When Doggett starts clawing at the freshly plastered wall, he does so at just below his eye-level and blood starts pouring from the hole he makes. The dead woman inside the wall was stabbed in the lower abdomen; there's no way that blood from the abdominal wound would've seeped through the wall at the level he was digging.
Continuity mistake: When the guy from the NSA is speaking with his supervisor, after the supervisor asks him about his wife and child, in the background he turns his head toward the supervisor, while in the next close-up take he turns his head toward the supervisor again.
Factual error: After a short examination of Shannon McMahon with a stethoscope and blood pressure meter Scully definitely claims that physically Shannon is absolutely normal. However, this type of examination cannot reveal any of Shannon's supernatural abilities. In order to prove or disprove that Shannon is a supersoldier, Scully could only examine if she could breathe underwater.
Continuity mistake: After entering the room with the water tank Agent Doggett has dived into, the Assistant Director Brad Follmer screams "Doggett!", while in the same scene in the "Nothing Important Happened Today I" episode he screams "Agent Doggett!"
Continuity mistake: When Scully reads the alleged printout of the email sent to her by Mulder, it says: "Dearest Dana: I've resisted contacting you for reasons I know you appreciate...I want to come home, to you, to William", but when Scully has previously viewed this message in the internet café, it had a different form: "I've resisted contacting you for reasons I know you continue to appreciate...I want to come home. To you, and to William."
Continuity mistake: During the previous episode, Skinner receives a nasty gash on his head courtesy of Billy Miles. This episode takes place 48 hours later and there is no indication whatsoever that Skinner received such an injury (the wound is visible once again in the next episode).
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.