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: When it's learned that Jonah has taken a flight to New York by himself, the panicked adults never think to contact United Airlines, the New York Police Department, port authorities, airport security, the taxi companies, or the Empire State Building staff to alert them that an unaccompanied minor child is headed their way. Instead, Sam hops on the next flight to NYC to search for Jonah by himself. Considering the many hours Jonah waits on the Empire observation deck alone, it is apparent that none of the above knew he was there.
Plot hole: In the scene in the hotel, David sees the victim's head on the floor after the killer left. Later when David is in a hospital bed he is watching TV and the reporter claims that all the heads were in Judd's car. The killer would have had to have gone back into the hotel room to get the head of that victim after David saw it. She would have put it in her bag right away if she was saving them all. The bag was even left behind. (01:12:30 - 01:25:00)
Plot hole: There's a number of strange things about Butch's and Terry's escape: When the grid falls down the very loud noise passes unnoticed. After they climb down the tied bedsheets Butch pulls once and it comes down, although no-one tied it loose. And finally, their escape route ended within the prison walls, and they needed to kidnap the clerk, who had come back into the prison to get some papers, for the escape in his car, something which wasn't planable at all. (00:05:40)
Plot hole: Towards the end of the movie we see Mr. Wilson peek out from his front porch, surprised to see Dennis biking back home with his wagon carrying Switchblade Sam, tied-up and partly unconscious. Either Dennis must have some hidden super-strength or knew how to tweak the laws of physics there is no way that an eight-year-old kid of his build could carry an adult of that size to his wagon let alone easily bike home with Switchblade Sam's weight. Plus being an experienced criminal like Switchblade Sam he may have offered some resistance in being caught doing so much less submit to a mere kid. (01:50:00)