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: 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: Michael McKean quits pursuing Beldar and approximately 15 years pass as indicated by Connie growing up, yet when you see McKean again and his assistant, they have not aged at all.
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.