The last scene in the movie, which shows the real-life Molly Craig walking with a walking stick, was shot first. According to Phillip Noyce, during an interview after a screening, Molly's age and health made it so that it would be best if that scene was shot first.
During the opening scenes of the movie the lizard that they have been hunting is killed and when they are carrying it back to their home the lizard is first carried one way then switches with the change in camera angle and then changes back.
When Moodoo is first seen riding north along the Rabbit-Proof Fence to meet a police constable he's on the west of the fence. Shortly before the actual meeting he's on the east side of the fence.
Far into the story the film shows the view from Mr. Neville's office window, allowing us to see a few applicants. Among those is a couple whose application had been rejected early in the story by Mr. Neville. Obviously the same set served different scenes that were far apart in time.