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: In Weekend at Bernie's one, Larry takes Bernie's watch and never puts it back on the body. In Weekend at Bernie's II, he gets the watch at the morgue after it's been taken off the body, and signs for it. How did the watch get back on the body?
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: 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.