Right before Lord Asriel is captured, he slides over a cliff of ice. In the first shot of him when he reaches the bottom at 42:11, he has a large scrape on one side of his face, but in the next and following scenes it is gone.
When Lord Asriel is walking through the snow, before he gets captured, he reaches with his right hand to pull down his goggles at 40:58. In a closer shot also at 40:58, it shows him pulling them off with his left hand.
The first shot of Lyra in the Experimental Station is a reverse angle of her walking through a doorway with double doors at 01:22:35. When the shot changes to the front at 01:22:42, the doors are closed.
When Mrs. Coulter is about to deploy the small robotic bugs to seek out Lyra, she says, "They'll seek her out like bees to honey." Bees do not seek out honey, they seek out the nectar and pollen to make honey. Nonetheless, "like bees to honey" is an old expression based on the affinity of many bees for anything sweet, to which those with an unguarded hummingbird feeder can attest.
When Iorek, with Lyra atop of him, is bounding across an arctic plain, the CGI breaks down for a second, for his left hind leg flickers as he runs.
Pantalaimon is able to transform into a small moth when he wishes. When he and Lyra are confined in the intercision machine, they are separated by a metal grid through which Pantalaimon in moth form could easily crawl: it is not clear what prevents him from trying this.
In the conference room where Lyra knocks the glass from Lord Asriel's hand, it falls to the floor and breaks. Almost immediately, the other attendees begin to arrive. Lyra goes and hides in the wardrobe and Asriel greets the attendees. None mention or even appear to notice the mess on the floor where Lord Asriel is standing. Even Fra Pavel who had poisoned it ignores it.