Visible crew/equipment: When Mulder and Scully enter the abandoned mine through a doorway, the viewer can see at right in the distance a number of people sitting on a wall, and one crouching in front of the wall with what looks like a dog. They are sitting still, but there is still movement there. (00:16:00)
Other mistake: Jack follows J. Edison Nash to a wine warehouse and watches as Nash punches numbers on a keypad in order to gain entrance to a private room. Nash punches the 6 and a beep is heard. He then punches the 8 and another beep is heard. During a close-up of Jack, four more beeps are heard, for a total of six. Jack says the number out loud - 862, which is only three digits.
Show & Tell - S6-E10
Continuity mistake: During a conversation with Diane, Jill says that her son is with his dad. In the conversation she calls the dad "Ken." In future episodes Jill's husband is called "Don." (00:03:55)
Ryuusui, Chimaera no Otoko - S1-E1
Continuity mistake: When Crosswords has the first attack of Chimera witnessed by Black Jack, his wife Sayuri runs to the fridge to grab the bottles. In the shot with the camera inside the fridge, there is a full complement of bottles in the bottom shelf, but in the other angle the right half of the shelf is occupied by glasses only. (00:09:15)