- Audio/visual unsynchronized: When Edwards moves the table during the "best of the best" test, the scraping sound begins before the table is moved.
- Audio/visual unsynchronized: Right before K unplugs the camera in the interrogation he says "Some night huh?" but his mouth is not matched with the voice
- Continuity: The shotgun Edgar puts down in the morgue disappears.
- Continuity: Kent Faulcon is identified as "1st. Lt. Jake Jensen" in the credits but calls himself "2nd Lt. Jake Jensen" in the audition scene.
- Continuity: The signs in the windows of the Russian restaurant change when shown from the inside.
- Continuity: The license plate on the LTD changes from centered to the right-hand side during the film.
- Continuity: When Rosenburg leaves his shop Edgar's "Zap 'em" truck is visible, reflected in the window. It is parked. The next shot of the street shows Edgar drive by and park in front of Rosenburg's shop.
- Continuity: When K and J are talking with Z just before the "skimmer" problem is identified, K's legs are alternately crossed/uncrossed between shots.
- Continuity: The address on the back of the MiB business card goes from being below the logo to above it.
- Continuity: When the Mets player is hit on the head with the ball he is wearing jersey #23. Later, when he is seen on the cover of the tabloid, he is wearing #20.
- Continuity: The first time we are shown Orion's belt, his name is spelled out in all upper case (ORION). However, when Dr. Weaver examines his collar on her desk, it is spelled out in mixed case (Orion).
- Continuity: When K is giving J his weapon, the bug's spaceship can be seen behind J before the shoot out at Rosenberg's.
- Continuity: When J and K shoot the space ship near the end of the movie, J is on the left side of K. When the space ship falls down, J is on the right side of K.
- Revealing mistakes: A pedestrian speed-walks past J's car window when they are first in the LTD, indicating sped-up film.
- Revealing mistakes: As J is being shown the screen where they constantly observe the aliens, the clips on the screen are being endlessly looped. A screen close to the center, for instance, shows a man getting comfortable on a couch over and over again.
- Revealing mistakes: When J is chasing the alien at the beginning of the movie, the alien leaps to the roof of the Guggenheim. When he does so the cables aiding in the stunt are visible.
- Crew or equipment visible: Partial reflection of the camera and its shadow can be seen when the camera follows the bank of lockers during J's initiation into the MIB.
- Crew or equipment visible: When K approaches Redgick's car, the shadow of the camera can be seen briefly.
- Crew or equipment visible: As J is trying to follow Edgar after the gun fight outside the jewelry store, the pyrotechnic devices used for the cricket gun damage blasts are clearly visible for a few seconds before they burn out.
- Factual errors: When K is looking at his wife via satellite, the view is horizontal, as though shot from the ground rather than "top down" as though shot from space.
- Factual errors: The exterminator's truck does not have a New York State DEC sticker, which is required for all pesticide application vehicles to have clearly on display.
- Errors in geography: When Agent K is looking up his lost love he types "Truro", then zooms in on Cape Cod. As he closes in, he misses Truro on the map by about 50 miles' drive (the town/village he zooms to is actually closer to Forestdale or Wakeby). Also the lush forest he zooms in on is all wrong; Truro has forests in the southern end of town, but of scrub pine trees, and North Truro is mostly dunes and grass.
- Errors in geography: As Darrel chases the alien at the beginning of the movie, the chase starts at Grand Central Station. In the next shot the alien is seen running downtown (the park is on his right) to get to the Guggenheim Museum. The Guggenheim is uptown from Grand Central.
- Incorrectly regarded as goofs: When the car is going super fast and upside down near the finale, J falls upside down and you can clearly see what appears to be a white leg. However, that leg actually is that of Will Smith (as shown on the DVD version's special features).