Continuity: In the scene where Will Smith throws a rock at the escaping Edgar alien, if you watch the rock after it hits the alien, it disappears after hitting the ground.

Audio problem: When Will Smith is looking at the two space ships at the MIB headquarters, if you look in the background Zed and K are there typing on the computer. But if you look closer you can tell that they're not even touching the keyboard and the sounds are just added into the movie.

Continuity: Just before the diner scene, where the two aliens are discussing the galaxy, we see the outside of the Russian restaurant. The neon sign says "haroshaya" meaning "good" all the way across the window, in the next shot inside the restaurant, the "ha", which looks like the English letters "xo", is gone and the sign is centered.

Audio problem: In the beginning of the movie when Will Smith first meets Rip Torn with all the other recruits, after he hands them the tests, look and listen very carefully. When Will pulls the table the noise for the table actually starts before he even pulls the table.