Continuity mistake: When M travels by train from New York to London, we see it crossing the Atlantic west to east. We then see it traveling east to west under the River Thames at Tower Bridge as it comes to a stop in London.
Continuity mistake: In the first movie, it is stated that the program was started in the '50s, but in this one it is stated that Gustave Eiffel was an MIB agent. He died in 1923.
Continuity mistake: When young M finds the creature, the rugby shaped plush toy behind it is either next to the edge of the table as seen in the wide angle, or away from the edge in the angle shot from behind.
Continuity mistake: When young M is woken up by the doorbell her right hand is either away or on top of the book, depending on the shot.
Continuity mistake: When M's dad shouts and scares her mom, her arm is either raised or lowered depending on the shot. (00:04:40)
Continuity mistake: When M walks to the HQ for the first time the street is in the shadows. A shot later the street is sunny.
Continuity mistake: When agent H is being chased by the MIB agents through the market streets of Marrakesh, he runs past the same extra twice in two separate streets: a young guy with a goatee, wearing a brown robe with red collar and a backpack. (01:02:00)