Continuity mistake: In the scene where Serleena confronts Zed in his office, look closely at her hands. Immediately after releasing Zed from her tentacles, her left hand now holds a box of Burger King fries, which disappear from shot to shot. This is most evident when she picks up the cellular phone, placing both empty hands on the desk first. (00:45:35)
Continuity mistake: In the scene at the lockers in Grand Central Station, Agent Kay takes his watch, an illuminated Hamilton digital, back from the little animals living there. In one shot, Agent Jay puts an analogue watch in the locker as a replacement, but in the next shot it is the same old Hamilton digital owned by Agent K. (This is mentioned in the DVD Audio Commentary with Barry Sonnenfeld). (00:51:15)
Continuity mistake: When Kay and Jay are watching the movie about the light, Kay starts to remember the real story and cries. The shot later, his is cheek is dry. (00:56:55)
Continuity mistake: When Agents Jay and Kay are in the elevator avoiding the garbage can robot who is shooting at them, watch their hands - they move from the wall to the roof ledge for support as the camera angle changes. (01:02:10)
Continuity mistake: When Agent Kay empties his guns shooting at the trashcan robot in the elevator, he throws down his guns and swings back to the roof of the elevator. When the robot moves into the elevator, the guns are nowhere to be seen. (01:03:00)
Continuity mistake: When Lara Flynn Boyle is holding up Tommy Lee Jones with her tentacles, in one shot you can see the tentacles coming out of her fingers, but when they show her up close, there are no tentacles coming out of her fingers. (01:04:15 - 01:06:45)
Continuity mistake: When Jay is in the fight scene with Jarra and his clones, Jay jumps up two clones to get to Big Jarra, but when the camera angle changes, the Jarra clone he jumped on is gone. (01:04:35)
Continuity mistake: In the scene where Jay is fighting with Jarra, we see the clear rubber tubes in very back of the room. After defeating all the Jarras there is only six seconds left to stop the launch. He could not make it from the back of the room to the rocket in time to stop the launch. (01:05:10)
Continuity mistake: During the fight scene with Jarra, Jay is dropped into the center of some large plastic tubing, but when the camera cuts to a closer shot, Jay is now seen at the edge of the plastic tubing. (01:05:15)
Continuity mistake: Throughout the whole movie when someone is driving they keep driving to different locations but if you look out the window it's just the same green background all the time. (02:27:09)
Continuity mistake: When J is trapped by the subway slime monster there are no cars on the left and a big mess is done on the curb and pavement. However, from the opposite side of the street, a frame later, the place is full of cars with no sign of the previous destruction.
Continuity mistake: When Jay and Tee first start to talk to Jeff, Tee grabs the "weed." When Jeff gets mad and starts banging on the grate, the wide shot shows Tee in the same position, gripping Jeff's weed, however it was not digitally added in that shot, so he's gripping nothing. But in the next shot, he's shown gripping the weed again.
Continuity mistake: When they land on the roof of the launch site, Jay gets out of the passenger side, even though he and Kay switched spots after which Jay was driving/flying.
Continuity mistake: At the post office, K waves his hands at J and turns around to where the employees are. When the angle changes K is waving his hands again.
Continuity mistake: Serleena's ship lands completely perpendicular to the ground, but when the angle changes it's pointing a 2 o'clock position.
