Plot hole: How did Professor Krassman get shocked into being a frog? The electronic device doesn't even touch his head.
Plot hole: Gail and Katie talk in her shed about Guy's phone call. Katie says "I didn't lie about anything", which is a really odd non sequitur. All Gail said was "I just got off the phone with Guy Morgan. Your phone. He just loved that little demo you left him. I have underestimated you. It'd make me proud if I actually cared about you." Nothing about it prompts a response like that, except the plot point that Gail told Guy that Katie lied about it appropriating Bev's demo. But Katie does not know that fact at that point. (00:21:00)
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: In the first film, the shape of the ring was a little different and it was set in a ring. Also, it was given to Xania. In the second film, she was never even acknowledged as donating it to the museum.
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.
Plot hole: The game in Houston is only 4 innings. If it almost got called after 2 innings, it's obviously pressed for time. Although called safe for the win, if Kelly was called out at home plate at the end of the 4th, the game would have ended in a tie. No extra innings would be allowed for sure this time due to time factor, so how would a winning team be determined to play in Japan?
Suggested correction: This isn't a plot hole, it's a question. Asking "what would have happened if..." isn't a valid plot hole. The writers had no need to explain "what if" scenarios since they never would have occurred. However, to answer your question with plausible answers; 1) The Bears HAD to win in order to go to Japan and thus a tie would mean the Toros played Japan (like a champion retaining his title after a draw in a title fight). Or 2) They played a 2nd game at a later time.
Plot hole: In the river scene, Betameche states that his pocket knife doesn't have rope, as it's only available on the smaller model. Yet, around 10 minutes later, Princess Selinia is pulling a retracting rope from the pocket knife, allowing them to abseil down. (00:45:00 - 01:00:00)
Plot hole: SPOILER ALERT! During the final fight, Joey kills Frank and she reverts back to human form. Abigail tells her she's fine, because Frank was the one who turned her. However, when Frank kills Lambert he does not revert back to human form, even though Lambert was the one who turned him.
Plot hole: During the bedroom scene, when Dennis shoves a flashlight into Mr. Wilson's mouth and nose, Wilson opens his eyes. It would be impossible for Dennis not to notice his open eyes, and realise he's faking being asleep, especially when he puts the light into Wilson's nose.
Plot hole: Emily begins to pull Henry out of the shed, but however there is no track leading to the other end. Also, the turntable is not big enough for both engines to fit on.
Plot hole: When Injun Joe is about to kill Huck, Tom takes notice of the chest full of gold coins and then empties the chest out (offscreen) because it was too heavy for him to lift, and then tricks Injun Joe into trying to retrieve the empty chest, resulting in Injun Joe falling to his death. The amount of time that passes between Tom glancing at the chest and then tricking Injun Joe before he can kill Huck is roughly 5 seconds. There's no way Tom could have emptied out of the chest in that little amount of time if the chest was too heavy for him to lift in the first place, especially without making a sound.
Plot hole: It's never really addressed or explained how Shredder survived his death in the previous movie from being crushed in a garbage truck.
Suggested correction: It didn't really need to be addressed, and thus is not a mistake. His hand emerging from the junkyard is enough to show that he survived his apparent demise at the end of the last film.
Plot hole: When Dubois attempts to kidnap Alex using the tranquilizer, she is brought to a halt by several different zoo staff thanking her for returning him. The entire first movie's plot is based on them being stranded on Madagascar after being on a ship that was intended to take them away. The actions of the animals at the train station were on the news, and a large gathering of sorts was held to show that the animals were leaving the zoo. Therefore, no one should have reacted this way to his return.
Plot hole: Pinocchio drowns even though he walked along the ocean floor with no trouble just minutes earlier.
Plot hole: In the series we learn that these creatures take a lot longer than us humans to grow up and that they live a lot longer. They mention that the children are about 900 years old, so a grown-up would be more than 1000 (probably 2000). The series is set around our time (1990s/2000s) and Fjellrose and Erke are very old. Yet the film is set about 100 or 200 years ago, you can tell by the way the humans are dressed and the way their houses are built etc. So Fjellrose and Erke should still be grown up, but they are young children. If they are only 100 to 200 years younger, then they should be much older in the film or much younger in the series.
Plot hole: At the very beginning, as the passenger ship is foundering in a powerful storm, the little boy places his kitten in a box and tucks the box inside his shirt just moments before he is cast into the churning sea. Sinking into the depths, the boy and other passengers are presently rescued by Captain Nemo's team of divers, who supply the drowning passengers with oxygen until they board the submarine Nautilus. Once aboard, the little boy opens his hidden box to reveal a wet but very much alive kitten that could not possibly have survived submersion for that length of time in a box that was not waterproof.
Plot hole: Mr. Cranston asks Denise to be the accompanist for the school's production of "Chicago". This is an error. In the year 2009, in which the film is set, this would be impossible since the licensing company which has the theatrical rights for "Chicago" restricts the show from being produced (even by amateur groups and schools) anywhere in the greater New York area while there is an open-ended production running on Broadway.