Plot hole: When (future) Agent J and (future) Boris are fighting on top of the large red docking station for the spaceship, Agent J gets shot deliberately by Boris and jumps off the edge of the dock. Then he uses his time travel device to go back in time a few seconds earlier to be able to dodge the shots. There are a few mistakes in this part. 1) There should be another Agent J and Boris there too, as they have gone back in time to that moment again. However in the movie there are only two of them. 2) The injuries sustained by Agent J (the bone spikes in his abdomen) should have remained there when he went back in time. If it were true that you healed once you went back in time into the condition you were in at that moment, then Boris should have grown an arm back when he went back in time. 3) Due to the time loop, Agent J remembers how to dodge the shots, while Boris doesn't remember anything and is surprised by the outcome. (01:29:00 - 01:30:10)
Plot hole: Lunar-Max prison is obviously part of MiB, them creating it for the purpose of holding Boris the Animal, and other criminals of worth as well. A high tech prison built on the moon with cutting edge technology and armed guards out the boot. Boris trashes the place, sounding all kinds of alarms and busting out, even blowing a sizable hole in the side of one of the complexes. He then jacks a ship off the moon's surface and crashes it back down to Earth. MiB doesn't know about it until almost a full day later when they realise the ship they found was from the moon, and Boris had escaped. It makes no sense that it took them that long to find out the information. A maximum prison, especially one to contain aliens on the moon, would be in contact with MiB. And any alarm that goes off there, especially for a break out of a high danger prisoner such as Boris the Animal, would have sent an alert to MiB headquarters right off if there was any logic to their system at all. There is only about a 1.5 second delay for a message traveling at light speed to reach Earth from the moon due to its distance. So within seconds of Boris busting out, MiB should have already been mobilizing to track where he would be going and intercept. There's no way, that logically, Boris could have escaped, made it back to Earth, and been there for nigh a day without MiB knowing about it and having their agents already tracking him down. (00:03:55 - 00:14:25)
Suggested correction: Boris made his escape and trip to Earth in a matter of minutes, of course MIB were tracking him in that time, it's just not shown on screen.
Plot hole: At the ball park stadium, K, J, and Griffin are high up in the bleachers watching a future window of the Mets game. Boris suddenly drives by on a motorcycle up in the stands and grabs Griffin, then plows through the railing on the side of the stadium and falls down below, crushing K's car. He then speeds off instantly out of the parking lot with Griffin. Then suddenly, somehow, J and K are running out into the parking lot close to their car quickly enough to be watching Boris speed away from the parking lot on the road. There is absolutely no way K and J could have made it out of the stadium and out into the parking lot in just a couple of seconds like that. (01:09:05)
