Continuity mistake: Approximately two scenes after Kitai leaves the pigs' burrow where he sheltered for the night, the "cutlass" is suddenly missing from his backpack. He later retrieves another from the ship's tail section. There is likely a deleted scene which would have explained the loss of the cutlass.
Other mistake: When the ship begins to crash, Cypher Raige tries to calm Kitai down and is violently pushed to the far left by the force of the ship accelerating. However, less than a few seconds later, the camera shows that to Kitai's right, the force is now tearing the back end of the ship apart and sucking people outside. This is contradictory because the massive air current resulting from the ship's acceleration would have either sucked everyone, including Cypher Raige, outside, or it would have pushed them inward, which we see with Cypher Raige. There is no way for the force to suddenly change directions within the same area of the ship.
Continuity mistake: Just after the other group of men say "Go easy on him, Sarge. That's the Prime Commander's son right there." 'Sarge' turns his head back to face the boy and has his head level, not moving. It cuts to a frontal view and suddenly his head is tilted to the right and moving around. (00:12:45)
Revealing mistake: Right after the huge bird soars back to the trees and Kitai begins to run along the river something has either been moved or cut from the scene...look almost to the bend in the river in the rocks.