Plot hole: Katherine (Kirstie Alley) the tooth fairy is instructed by Rodgers (Lynn Redgrave) that she can only go out at night, otherwise she stays in an apartment in Limbo to get her assignments. She is given names all over the world. There is always a part of the world that is in nighttime. She should always be working and never at Limbo.
Plot hole: When the policemen walk through the warehouse and see the bloodstains from the dinosaurs killing people, Captain Polaris asks Runaway to come with them and help. This makes very little sense, as Runaway and Ann have just been arrested by the police (for no apparent reason) and Polaris does not know that Runaway is from the cyborgs planet and therefore has knowledge about the dinosaurs.
Plot hole: Al Simmons' reasoning for wanting to quit A-6 is because he learns his rocket attack in his assassination mission in the beginning of the film yielded civilian casualties. This makes no sense, as he blatantly gunned down several innocent men in the air control tower just moments before.
Plot hole: In the waning seconds of the championship game, the Huskies are down by 2 and UMass has the ball. Not only do the Huskies not intentionally foul to stop the clock, but UMass attempts to run a play and set up a basket when they simply could have dribbled out the clock and won the game. Both these strategies go against what any basketball team would do in this situation, especially in a championship game.
Plot hole: Kahn's death makes no sense. In the film, Rayden explains that the dragon tattoos flee one's body upon the person dying. And yet, Kahn is still alive and not even close to death when his tattoo flees. (Which is what kills him, since it rips him open when it flees.) It's like they couldn't figure out how to kill him in the script, so he's just spontaneously is killed by his tattoo, even though it violates the rules the film set up.