Male Marty is seen in the left hand corner after female Marty exits the car for the officer.
When the team is examining the first corpse, the eye twitches (time between 5:15 and 5:25).
At around 40:00, when Mulder and Scully break into a hotel room, a silhouette can be seen dropping down behind the window. It could be falling equipment or a crew member ducking out of sight.
A brief scene of Mulder and Sculley driving to Massachusetts shows mountains in the background that clearly are nowhere near New England, but are the mountains of British Columbia.
There are no nightclubs in Germantown, Maryland.
If you look carefully around 5:20 into the episode, when Muller is taking samples from the dead guy, you can see the "dead" guy blink.