Continuity mistake: Mulder says that Scully was abducted and missing for four weeks. In "Duane Barry," the date stamp is given as August, then in "3," when Mulder returns to the X-Files office he turns the calendar all the way to November. Since Scully is returned the next episode after this, she must have been missing for at least 3 months, not 1.
Continuity mistake: When the bank manager goes to open the door for the brinks truck containing the robbers, the clock on the wall reads 9:45. When the robbers are taking him back to the vault, a couple of shots of the skull-masked robber shows the clock reading about 9:43.
Continuity mistake: At the end of this episode when Mulder is talking to Marty through her jail cell, the position of their hands change. In one shot, Mulder's hand is covering hers, and in the next, each of their hands are gripping the cell bars. This goes back and forth a few times.
Continuity mistake: This is probably one of the most intriguing chess plays in the history of mankind. In the first move shown on the screen Gibson moves a white knight from e4 to f6. Then, in the close-up, the situation on the chessboard more or less corresponds to the arrangement of the figures previously shown on the screen. However, in the next shot, when we see the chessboard from the Russian perspective, the arrangement is completely different. Especially, there is no white knight on the chessboard at all. In the following shot the white rook suddenly appears on g8 (and is subsequently beaten by the black king), but in the next move Gibson again moves his white rook on g8, while the black king has miraculously returned to h8 and again beats the white rook. Moreover, Gibson could not play two white rooks, because later on we see that there is still at least one white rook on the chessboard.
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Continuity mistake: When the CSM discovers the bright spot on the carpet, he immediately realises that Mulder's apartment was under surveillance. However, one can notice that soon after entering Mulder's apartment, the CSM looks down at the floor and carpet covered with blood and there is no bright spot.
Continuity mistake: When the Lone Gunmen speak with Susanne Modeski, in the background there are some cars parked in front of the Stadium Inn. However, just seconds after, when the telephone rings, there is a white truck parked at the entrance. Later on, the cars are back again.
Continuity mistake: Izzy unwraps a peanut butter sandwich and sets it on a bare tree stump as bait for 'the Great Mutato', then he steps away with the others. When we see the Great Mutato hurriedly put it down, a paper bag is suddenly sitting on the stump beside the bitten sandwich.