Plot hole: Stephen dies after he was "taken off machines", at least so his wife tells the kids. But when he was shown in the hospital he was attached to no life-supporting machines except an oxygen tube in his nose. (01:33:25)
Plot hole: This TV movie uses a lot of flashbacks to the previous 4 installments, by having people saying to each other, "Hey, remember that time when we..." a bit more than usual. In the village of the Minotaur, Iolaus remembers the fight from Hercules and the Amazon Women where he dies. That is also the reason why this flashback is interrupted just before that point. But at the end of the Amazon Women story Hercules used magic to jump back in time and change history so that the whole adventure had never happened (next making sure that it would not happen all over again). Obviously they wanted to use some cool action footage from all the TV films. But Iolaus could not remember these events as it happened in some cancelled version of the future. (Hercules remembers, but he wasn't going to tell anyone, and that's what we have to go on).
Plot hole: Towards the end of "The NeverEnding Story 2", Bastian's dad became aware of his son's adventures in Fantasia. Yet, in this film, he reacts to the news about Bastian stealing the NeverEnding Story as if he's never heard of the book before. Adding to that, he does not recognize the Auryn on his son's sweater nor does he know what it can do.
Plot hole: When Joe takes Black Beauty and Ginger away from Birwick Park to their new home, he is about 11 years old. When next Beauty sees him at the fair, he has aged to his early/mid twenties. This would indicate that Beauty had been at the home of the Lord and Lady Wexmire for about 10 years but not a single character in the household ages a day during his time there. His stay would appear much briefer than that.
Plot hole: When Picard is talking to Guinan inside the Nexus she tells him that he can leave and go anywhere anytime and Picard and Kirk go back to Veridian III just before the launch of the missile. Now why didn't Picard go back to when they first located Soran on the Armagosa observatory and detain him there? Or if he wanted to he could have gone back even further to Earth and saved his brother and nephew.
Suggested correction: This is a question, not a plot hole. Characters behaving differently than you would doesn't constitute a plot hole, and there's nothing contradicting the plot. The short answer is because of the Temporal Prime Directive. Yes, there have been several Star Trek episodes and movies dealing with time travel, but Picard knows it's best not to change the past too much. Plus, going back even further in time doesn't guarantee he'll be able to stop Soran.
Plot hole: There is a scene setting up the nonsensical resolution of the plot, when the policeman recaps the various baby sightings. First; he already got 'fake' reports he chased, there was a scene about that, let's ignore the fact that certainly he would have gotten more like that and he conveniently for the plot lists just the few relevant ones. Second; the baby was kidnapped at 10 and the baby sighting on the bus happens "in the morning." Then the zoo sighting happens "at 3 o'clock." The construction site closes at 5 o'clock. Even forgetting the superior stamina of the 9 months baby that has been walking a whole day without a break, that's a lot of stretch for the actions as shown in the movie, in particular the time between the bus and the zoo; the bad guys would have been loitering in search of the baby for hours between the bus incident and the moment when he leaves the department store to get to the zoo.
Plot hole: Harry goes into the Mall, and two of the terrorists follow him through the Mall, up the escalator, down the hall, and into the men's room. Then the third terrorist leaves the car and follows exactly the same path to where the other 3 went, even though there's no way he could have known exactly where to go.