Plot hole: The whole plot of the first "Brother Bear" was that Kenai had to go to that mountain to become human. But at the end of this movie, the spirits were about to change Kenai back into a human in the middle of a cliff, which makes the entire first movie completely pointless.
Plot hole: At the end of the movie, when the water drains away, there would be no way for a) the amount of water to drain away that did and b) for the mammoths that came through to be completely dry. (01:16:20)
Plot hole: It would have taken much longer to build the 54 acres of homes than the animals hibernated, so there's no way they couldn't have known what was going on around them.
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: 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: Cruise leaves Lugnut to go buy he and Coupe some seats and mere seconds after leaving, Coupe appears in the scene and talks with Lugnut. Coupe asks if he has seen Cruise, but even if Cruise had already left to go buy tickets, Coupe would have already seen him when approaching Lugnut since she only arrived seconds after he left. (00:09:15)