Plot hole: During the climatic battle in the snow, Lyra Belacqua is about to get shot by one of the soldiers, and Iorek Byrnison comes to her rescue and is able to surprise & kill the soldier. The problems with this is where Iorek appears would have been right in the line of sight of the solider, and bearing in mind that Iorek is VERY big, wearing armour so as not to blend in with the white surroundings, and making lots of noise, it would have been impossible for Iorek to stealthily appear from nowhere.
Plot hole: Harry can now see the thestral creatures because he witnessed Cedric Diggory's death in "Goblet of Fire." However, he should have been able to see the thestrals after Professor Quirrell died from Harry's touch in "Philosopher's Stone". Quirrell crumbles into dust (dying) while Harry is still conscious, watching, and fully aware of what he is seeing, thus allowing it to fully sink into his consciousness. Harry faints "after" Quirrell is dead and as Voldemort's spirit passes through his body. Nor does it only have to be a friend or loved one who dies before the thestrals can be seen - it can be anyone, including an enemy like Quirrell. There only has to be an emotional response to the death, which can be love, hate, fear, shock, etc. (In the book, Harry did not see Quirrell die, but that's irrelevant to the film).
Suggested correction: JK Rowling has said that in order to be able to see thestrals the death has to "sink in" psychologically with the person. Which was her explanation for why he couldn't see thestrals even though he witnessed his mother's death. Given Harry's age and the way Quirrell died, it is possible that Quirrell's death didn't have enough of a psychological impact on him to "sink in." After I first personally witnessed a violent death, I didn't feel the impact until a few years later. It can take time.
Plot hole: Vanessa seems upset at Barry when their actions at getting the honey back from the humans result in the flowers and other plants dying. One might think that Vanessa, as a florist, would know the outcome and would warn Barry instead of helping him with his plan. Yet she appears to blame him for the entire outcome when it becomes apparent.
Plot hole: In the scene with the brothers group, the guys don't believe that Fred is Santa Claus's brother (because they don't believe in Santa). But why don't they believe in Santa? Santa leaves gifts for kids on Christmas. If they don't believe in Santa then where do they think the presents came from?
Plot hole: When the chipmunks finally release their first song, there is a montage showing the chipmunks rising musical success. In one shot we see a marquee promoting "The Chipmunks Premiere CD Release", and on it is a picture of the chipmunks in the clothes Dave has made them (note Alvin in his 'A' jumper.) However, Dave doesn't actually make the chipmunks these clothes until further on in the film. (00:41:50)
