Some minor mistakes uncovered.
Errors in geography: In numerous episodes in the earlier seasons, characters are seen driving cars with British Columbia License plates.
Errors in geography: On at least one occasion the scene location title gave the location of a scene as being in "Silver Springs" Maryland. There is no "Silver Springs" Maryland; the proper name of the city just north of Washington DC is "Silver Spring" - singular not plural. There is, however, a "Silver Springs" in Florida.
Revealing mistakes: When the medical examiner at Bethesda Naval Medical Center removes the sheet off of the corpse of the first thug, it briefly reveals that he is still wearing boxer shorts.
Errors in geography: Dr. Kurtzweil's office is located at Dupont Circle in Washington, DC. However, when the police search it, some of the officers are wearing patches of the Arlington, Virginia, police department.
Continuity: Gelatinous red goop on Scully's gloves in the autopsy scene.
Continuity: Mulder's mobile phone changes from a non-telescopic antenna type (presumably as a Nokia product placement) to a telescopic antenna type while he is in the room with the drink dispenser bomb.
Continuity: After Mulder is shot, he has a wound on his temple. The wound disappears in Antartica and reappears after the hearing at the end of the movie.
Continuity: As Mulder and Scully are climbing down the rocks above the corn field, she is wearing flat-soled shoes. When they enter the beehive, she has high heels. (And not a scratch on them either!)
Factual errors: Most cell phones won't work if they're in a metal room in a big building.
Continuity: For a close-up shot where Scully probes a fireman's corpse, she appears to be wearing a white lab coat that she's not wearing in longer shots in that scene.
Continuity: Mulder has gloves on when he falls down the ice chute in the Antarctic, but the gloves mysteriously disappear when he comes out of the chute into the main spaceship area.
Continuity: When Mulder discovers the bomb in the vending machine, the door to the room gets knocked down. Later, when Michaud is "disarming" the bomb, the door is back up.
Continuity: When Mulder falls down through the ice the hood on his coat falls off his head yet the next scene he is seen pulling the hood off his head.
Continuity: In the scene at the railroad crossing the train has 3 flatcars with tanker trucks on them. In the next shot as the train enters the tunnel there are only 2.
Revealing mistakes: In the cornfield the domes are obviously lit from the inside. Once inside the domes it appears they are lit from the outside, primarily from lights near the ground.
Continuity: When Kurtzweil is talking to Mulder, Mulder's cab arrives twice.
Continuity: The snow vehicle that CGB Spender rides out to Mulder's vehicle has long parallel treads. When he is driving back to the base, the tracks shown are the treads on Mulder's vehicle.
Errors in geography: The coordinates that the Well-Manicured Man gives Mulder to locate Scully are not in Wilkes Land. 83 degrees latitude South & 63 degrees longitude East are indeed in Antarctica but hundreds of miles from Wilkes Land, closer to the South Pole.
Errors in geography: In the scene in "North Texas" where Dallas can be seen in the distance, the surrounding area is dusty, treeless desert. The real areas in Texas where Dallas can be seen in the distance are live-oak covered wooded areas or large, sprawling suburbs.
Continuity: When Mulder and Scully enter the bee dome, Mulder's tie is alternately neat/over his shoulder between shots.
Factual errors: The movie takes place in July but during the sequence in Antarctica the Sun is up (fairly high). During July, the Sun never rises in Antartica (at least not at the coordinates given by the Well Manicured Man).
Continuity: When Mulder and Scully run out of the domes to escape the bees, Scully takes off her jacket to pull it up over her head twice.
Continuity: At the railroad tracks, the car has its parking lights on as Mulder and Scully stand outside, watching the train pass. In the next shot, the headlights are on.
Errors in geography: When the helicopter is flying through Dallas, it passes the "One Wilshire" building in Downtown L.A. As it lands, the building to the right bears the "Pacific Bell" logo which would not be found in Texas.
Factual errors: It would be almost impossible to go to the interior of the Antarctic continent in July (middle of the winter) due to extremely bad weather. Barring extreme medical emergencies, no U.S. flights land on the continent between April and October.
Factual errors: It would be mind-numbingly cold in the interior of the Antarctic continent in July. Given the meager clothing that Mulder was wearing he would have been hypothermic and frostbitten very quickly.
Continuity: In the limo where the well-manicured man shoots his chauffeur while sitting beside Mulder, you can see Mulder lowering his arm while holding the vaccine immediately after the shot. But in the next scene, both of Mulder's arms were raised.
Continuity: After Scully gets stung by the bee in the hallway, Mulder rushes back into his apartment and dials 911, while through the windows you can see that it is still daylight. But when the paramedics load Scully into the ambulance waiting outside, it's now almost full dark.