When Mulder tells Scully he is sorry about her father's death, he puts a hand on her shoulder and moves it up towards her cheek. In the following shot, his hand is moving down towards her cheek from her temple.
During her father's funeral, Scully tells her mother "As a Captain he was eligible for burial at Arlington." Rank has nothing to do with eligibility at Arlington Cemetery.
Mulder sarcastically tells Scully that he had Boggs channel Jimi Hendrix, and mentions Hendrix having been dead for 20 years; Jimi Hendrix in fact died approximately 23 years prior to this production.
When Scully swiftly leaves Boggs' interrogation room, the elbow of a crew member trying to hide against the wall is briefly visible as she rounds the corner.
When the police officer assisting Scully in the investigation of Mulder's shooter gives a history of the suspect he completely mispronounces the name of the prison where the suspect had been incarcerated.
This is very odd as "Angola" the prison name, is the same name as a nation in Southwest Africa. It's as if the speaker had never heard of either of them and had never spoken the word prior reading it from the script.