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.
The bush they hide behind when they meet the friendly bushman is the same bush they hide behind later when avoiding the tracker.
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.
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.
The three girls Molly, Gracie and Daisy were not taken by surprise and removed by force from Jigalong. The violent removal scene in the film is entirely fictional. The girls' mothers were informed beforehand they were to travel with Constable Riggs and, without any protest, they acquiesced in the decision. The girls left Jigalong on horseback, not locked in a motor car.
The speech in the film to a Perth ladies charity society by actor Kenneth Branagh, playing A.O. Neville, was never made by the real Neville. The words did not come from a transcript found in any historical archive but were created for the film by screenwriter Christine Olsen.
The Moore River Settlement was not, as the film portrays it, a prison, nor was it solely for children. Aboriginal people went there voluntarily and temporarily to gain access to welfare and services. Between 1930 and 1934 Moore River admitted 1067 people, but over the same period 1030 people left.