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).
Continuity mistake: After Jay and Kay go to see Jeebs about the deneuralizer, Kay leaves and the bad aliens come crashing through the walls. Jay shoots Jeebs head off and, as it's growing back, he says he got shot "right in the pie-hole" (mouth). However he was facing away from Jay when he was shot and it was above the mouth area.
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.
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.
Continuity mistake: When Jay and Kay make their visit to Jeebs, Jay is talking to Jeebs and you see Jeebs making a statement about how his business is 'banging' and when he see Kay walk in, he points both his hands at him. The camera angle changes and Jeebes is now seen with only one hand pointing at Kay.
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: The entrance room (the large stone building off Battery Avenue) to the starport reverses between the two movies. In the first movie, the guard sits on the right hand wall as one faces the elevator, with a fan visible through a grille behind him, and a circular vent on the other wall. In MiB II, he is sitting against the left hand wall, but the fan and grille is still behind him, meaning it has changed walls.