Plot hole: Frankie makes reference to fear of fire early in the movie in the scene with all the guests arriving at the hotel. And in the scene in the local village with the monster festival, a single match is used to send him on a rampage. But throughout scenes in the hotel itself, there are lit candles, candelabras and torches throughout, most noticeably in Mavis' room during the scene where her monster friends (Frankie included) are addressing her idea of going to a human village. None of this fire affects Frankie at all.
Plot hole: When the aliens kidnap the adults, the kids are left behind. But all the kids seen are around 11 and younger. Where are the teenagers or young adults? None of them are during the celebration scene nor in the arena on the alien planet.
Plot hole: Mater tells McQueen he moved and looked like he just saw the Ghostlight. Sheriff gets on to Mater for talking about the Ghostlight and then their whole plan falls into place to trick and scare Mater with the blue lantern. Only there's no way they would have known that Mater would have mentioned the Ghostlight after that. McQueen didn't know about it, supposedly. And he had been scared by Mater and had been there enough that he would have known if Mater had mentioned it before, and Mater would have known he told McQueen. (00:01:55)
Plot hole: Gerry's wife uses a rocket boot to break through a window and then slides down a curved wall to get to their son. She does so gracefully and takes off running. Gerry slides and takes a hard tumble and rolls down, landing on the ground. The next shot shows Gerry running behind his wife and not too far away as they reach their son. Even if it was to show a little time passing, there was not enough distance between where they broke the window and their son for Gerry to have picked himself up and catch up to his wife before reaching their son, especially with his wife being a worried mom doing a full on sprint to her kid.
Plot hole: Batman finds at Belson's home a handwritten list of substances needed for a transplant. Why would Belson, a medical authority in the field that knows those things thoroughly, even write a list down? If it's for Freeze to procure him the material, why would it be at his house and not with him, and when did he even have time to be at home to do that, since he has been kidnapped by Freeze when he was driving on the outskirts of Gotham and taken to the oil rig? If he had time to go home, he at least would have changed clothes, he's still in the tuxedo he wore when he was kidnapped the night before.
Plot hole: The main plot of the film involves Iris and Olson's mission: Destroying the Mobile Fortress 000. But Iris is a special gynoid. Her primary function is to activate the Mobile Fortress. The antagonist of this film could unleash calamity if he had Iris and the fortress. So, which idiot has sent Iris on this mission? The logical course was to send a demolition team, or better yet, send no-one at all. Anything is better than sending the activation key outside the safety of the Olympus.
Plot hole: When Karate Kid accidentally frees Lex Luthor from the ice in the future, Lex just hops up with no problem and starts walking around perfectly fine after being frozen solid for 1000 years. Yet when they go back in time and then later free him from the same ice in the past, Dawnstar has to revive him so he can get up, and even after being revived, he is weak. Yet in the future, he came out of the ice perfectly fine and stole the Time Keeper. (00:11:10 - 00:37:20)
Plot hole: When the dome of crystal collapses, all the animals inside immediately grow old, including Brook, implying that the magic from the crystals is completely gone. However, when a tiny piece of crystal lands in the hot spring, it creates a 'fountain of youth' which the animals then bathe in to regain their youth. If that little piece of crystal worked, then why didn't the many crystals from the broken dome still work? Also, how is Brook able to leave the fountain of youth and go looking for Sid at the end of the movie without growing old?
Plot hole: After being hit with the spores, Cobra Commander cannot walk or even move very well with any speed at all. The Cobra minions have to drag him to their prison with the Joes and just leave him there on the ground after the Joes make a break for it. The Joes go quite a distance to engage Cobra. Road Block is delayed only a couple seconds behind the other Joes when he is grabbed, but knocks out the minion who grabbed him. Suddenly, Cobra Commander is at his feet telling him to wait because it's a trap. Later, Road Block has to carry Cobra Commander because he still can't move much. There's no way Cobra Commander could have caught up with Road Block to warn him of the trap. (00:52:50)
Plot hole: Nick Fury wants to detain Tony as he is the only witness. Tony takes off and Nick Fury even says to apprehend him so their only witness isn't killed. Yet when the S.H.I.E.L.D. robots confront Tony at Pepper's vacation spot, they say they are authorized to use deadly force against Tony. And Nick Fury even orders them to fire when Tony resists. If they need Tony to keep their only witness alive, why try to kill him when he doesn't cooperate? (00:31:05)
Plot hole: Perhaps the biggest plot hole in the movie is centered about the reappearance of the Owsla officer Holly. Even if the warren was destroyed right after Hazel's band had departed, Holly would not have caught up with them right before the new warren at Watership Down - even with the delay at Cowslip's warren - with the additional detour in Efrafa, considering that acquiring the amount of information he got from its organization would take more than just one or two days. In addition, Richard Adam's novel, on which this movie is based, features the location of Efrafa some distance away from the down, nowhere between it and the Sandlefort warren (Hazel's and Fiver's home). In fact, Holly went to Efrafa (along with a missionary group of Hazel's band) some time after they had settled down in the new warren.
Plot hole: It's one thing to have a small amount of liquid nitrogen (about the size of a standard propane tank, by the looks of it from the Fridge scene), but where did the gallons upon gallons of it during the climactic flood scene come from?
Plot hole: In the scene where the Sheriff stops the cows' brawl, he gives them to the Chinese man. The Sheriff knows what Pearl's animals look like, so why didn't he recognize the cows as Pearl's?