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.
Continuity mistake: When Lee Scoresby is talking to Iorek on Lee's balloon, Scoresby runs his fingers through his hair to pull it out of his face before he puts his hat back on. After replacing his hat atop his head, he brushes a few stray hairs behind his left ear. The shot briefly cuts to Iorek, then back to Lee. More hair than he originally had to tuck back is covering his left temple.
Other mistake: In the last battle scene, the same death is shown twice. Just before 1h32, a Magisterial guard slumps towards the left foreground, his daemon bursting into dust from the right; and two minutes later just before 1h34 the same piece of footage is shown again.
Continuity mistake: In the last battle scene, Serafina kills one soldier by flying down from the sky and kicking him. In one of the shots, a body of a dead witch is a few meters behind this soldier. In the next shot, the body disappears, only to appear again a minute later in another scene with Serafina at the same place.
Continuity mistake: In the scene when Lyra and Pan are looking for a robe to steal, the conference room they enter has only a tray of glasses on the table. However, when the lord and Magesterium agent arrive, the bottle of wine later poisoned appears with no explanation, as none of the three men seen entering are carrying it.
Continuity mistake: When Lyra is walking through the palace to meet King Ragnar of the Ice Bears, there are a great many bears all around her, with a few following her right up to the king. She gets to the king, and when the shot pans out to the hall, suddenly all the other bears are gone. Even if they all left the hall, it would take more than a second or two to do so.