Plot hole: In the Cowboys' last possession of the final game, Spike makes a long run before being stopped on the goal line. The Cowboys' next play is a run up the middle. The Little Giants stop the run and the Cowboys lose possession, but since that was the first possession of a new set of downs, the Cowboys would have three more chances to score.
Plot hole: When the 3 ninjas' Grandpa is in hospital, he phones them and complains that no-one at the hospital speaks English. Not only is this a strange complaint to make about a hospital in Japan, but later in the film he is seen speaking in Japanese. He should therefore be able to easily communicate with people at the hospital.
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: 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.