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.
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.