When Brom and Eragon stop and get off their horses (after fleeing the Ra'zac, before Brom inspects Saphira), both can be heard referring to Saphira as "her" once and "she" three times during their dialogue. However, both of the characters clearly mouth the words "him" and "he". The sound was obviously re-dubbed. Additionally, there are one or two instances of missed dubbing, and either clearly refer to Saphira with male pronouns.
When Brom and Eragon are riding to Daret, it can clearly be seen that Brom is leading the way. Then, in a shot when the camera flies over the two riders from behind, it is Murtagh riding instead of Brom. You can tell by the larger cape, longer hair, and the fact that he is carrying a bow, which Brom never had. Then in the next shot it is Brom again.
When Murtagh and Eragon are brought to Ajihad, Murtagh stays on Eragon's left for several camera angles and shots but when Eragon turns around to call in Saphira, Murtagh is on Eragon's right for the rest of the scene.
In the beginning when Eragon and his uncle are talking while brushing the horse, as the camera cuts back and forth between the two, Eragon is holding hay in his hand that's on the horse - then he's not - then he is - then the hay is gone at the end.
When Nasuada and Ajihad are showing Eragon around, Nasuada's dress collar is on one side. Then it shows the scenery, then it goes back to the 3 characters and Nasuada's collar had moved to the other side, then the camera Nasuada's collar is back to where it was at the beginning.
About 40 minutes in the movie, during a riding scene, the CGI hills in the background are not synced correctly to the camera motion, giving the impression that the hills are actually moving against the foreground.