Sergeant Hynek is wearing a US Army name tag on his outdated USAF uniform.
At about 14:02 when the Abductee covers his face in fear, the metal bar that imprisoned him actually bend outward as his weight is pressed against it.
When the Man In Black rips open the VCR, the tape inside is shown to be fully rewound showing that it hasn't been played, yet Blaine was watching the tape just prior to answering the door knock.
At 36mins 40secs, Mulder puts his hand in an ice bucket the morning after the night before. The amount of water left would indicate the original ice filled the bucket to beyond overflowing, and that there was perhaps no bottle in the bucket either.
At approximately 29 minutes into the episode, an a trio of Air Force personnel walk up the hall to talk to Mulder and Scully. The leader of the team, Master Sergeant Hynek, is wearing obsolete rank insignia. The episode aired in 1996, and, one can assume, was filmed no earlier than late 1995; however, the USAF changed the MSgt. rank insignia in 1991, from six downward rockers, to five rockers and one upward chevron. By long before '95 or '96, all personnel would have transitioned to the new insignia.
At the end of the episode, as Jose Chung is narrating the 'where are they now' part of his book, the camera zooms out from Chrissy sitting at her desk. As it does, the arm and sleeve of a crew member can clearly be seen to the right of the screen.