Plot hole: The opaque red lined map that Otomo retrieves from his first fight is ridiculous. Why would people who know where the hidden base is be carrying around a map on them (which shows a route so basic that they'd have to be brain-dead not to be able to remember it anyway) just so that conveniently one of their enemies can get it?
Plot hole: This happens after Gabe has killed the guy in the cavern and is reaching for the radio. We hear Frank trying to reach them, so they must be on the same frequency. Then, Hal finds out that a bomb has been planted, grabs a radio from the bad guys and starts yelling for Gabe to get out of the cavern because of the bomb. Why didn't Frank hear any of this on his headset?
Plot hole: A nuclear armed stealth fighter is accidentally sent back in time to 1940's Nazi Germany. After the Nazis capture it, two days later they drop a nuclear bomb on the United States. There are several basic problems here. Firstly, if the Nazis captured advanced technology, wouldn't they spend more time taking the plane apart and interrogating the captured pilot? How on earth did they manage to train a pilot to fly the stealth in such a short length of time? And how did the stealth fighter manage to reach the U.S. from Germany when in-flight refuelling was unknown then?
Plot hole: When Spartan jumps through the window in the excavation scene of the museum, he crashes into a room with bottles of drink on the shelves. Surely this room too would have been filled in and the window smashed during the earthquake, and the museum wouldn't have bothered to excavate it as it can't be seen from above due to the blanked out window. So what is that room doing there? (00:49:20)
Suggested correction: It is not an excavation. It is only made to appear like an excavation for the museum; it is all decor to display the 20th century items like the car.
Plot hole: After Steven breaks out of prison, he goes to Jason's home. Then Jessica's boyfriend shows up talking on the phone and he says he will ask Jessica for permission to shoot their show at Jason's house. He should know that Jessica doesn't know she is a relative of Jason.
Plot hole: It is firmly established in the last half of the film that movie characters and movie weapons do inflict damage and death in the real world. However, early in the film, a bundle of dynamite comes straight through the movie screen and explodes in the real world movie theatre. That quantity of dynamite should have gutted the theatre, easily; but, when Danny Madigan and Jack Slater cross from the movie world back into the real world, there is absolutely no damage to the theatre.
Plot hole: Foster served in the military and even received a Purple Heart as indicated by the plaque in his mother's home. Yet he needs a kid to explain to him how to handle an M72 rocket launcher. A weapon introduced in the 60s and thus well within his time at the military.
Suggested correction: Not everyone in the military knows how to use this particular type of weapon. In fact, probably most don't.
Plot hole: April and Kenshin switch place in time as they were - by some extraordinary coincidence - holding the scepter "at the same time" (if the concept makes any sense) in the exact same pose, with a switch that takes several second of intense lightning storms and 'tornado weather' as one of the Turtles put it. Here there is the assumption that 4 priests would be around the scepter exactly at the same time, and when the Turtles do switch with Norinaga's elite soldiers instead they certainly were in completely different poses, far away enough to ride horses, who did not get spooked one bit by the lightnings and sudden winds but rode as if nothing happened.