Plot hole: In this movie Goblin was able to sneak up on Peter. But in the previous movies Peter was able to sense danger from quite a distance away; Green Goblin from a few blocks and the train barricade from over a mile.
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).
Plot hole: When they are swimming and before the family shows up, the Wild Hogs throw all their clothes on to the side of the pool. When the family gets in and they get caught, the mom seems to see the clothes from across the pool but she is looking the opposite way of where the clothes should be.
Plot hole: Landy uses the code 4/15/71 to point Bourne to the training site address. But how does he know it is on the East side?
Plot hole: I can somewhat understand that in a kiddies' show all aliens can inexplicably speak English - but using Terranean (i.e.: Arabian) numbers as well? While Tetrax's computer uses alien runes, the readout on Gluto's holographic HUDs use Arabic numbers - somewhat a bit too deliberate a producer choice to emphasize intergalactic communication.