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: In order for the treasure trail to be followed both desks would need to have existed in 1865 when the code was deciphered. However HMS Resolute wasn't broken up and made into desks until 1879.
Suggested correction: In the movie, the code-written in the 1860s-leads to Laboulaye's lady, which was already conceptualised in 1865. The statue, which was theoretically inscribed after the Resolute wreck was made into desks, then points to them.
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: Goob could not know how to use the time machine.
Suggested correction: DOR-15 is a sentient AI. It could probably figure it out and let him know.
Suggested correction: This is a baseless assertion, and therefore not a valid entry.
Plot hole: At the end, none of the duplicate Benders that are waiting in the limestone cavern under the Planet Express building have had their Obedience Virus or the time code deleted from them. There should have been only one Bender without the Obedience Virus, not all of them.
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.