When Willow gives Elora to Madmartigan, what is heard is, "Goodbye, little one," when originally, he said, "Goodbye, Elora." It was after the scene was shot that the people realized that Willow didn't know Elora's name at this point.
After Madmartigan rolls down the hill inside the giant snowball, a watchman shouts out that the soldiers are coming. Given how long and fast it took them to slide down, how did they get there so fast? Also, you hear clear clip-clop hoof-beat noises from the horses as they trample through loose powdery snow.
In the opening scene, immediately following Elora's birth, Sorsha is speaking with a woman who sounds suspiciously like Bavmorda, and states, "She bears the mark." However, Sorsha leaves the cell saying, "I must tell my mother," which would imply that Bavmorda was not present in the cell. Further, the only two remaining people in the cell when Sorsha leaves (aside from the infant) are Elora's mother and the midwife, neither of whose voices sounds remotely like the woman's voice heard earlier. This would suggest that in an earlier version of the script, Bavmorda was intended to be in the cell when the child was born, but the scene was changed later and the dialogue not re-recorded.
After the cart chase when Madmartigan and Willow get off the cart with the two back wheels missing, the rubber stunt wheel used to allow the cart to roll is visible in the center of the axle as it moves away from the actors.
Willow's hair is wet when he returns from the island. In a deleted scene, Willow was caught in a massive storm and went underwater. While we do not see this in the main movie, we can infer that it happened none the less.
Scratches inexplicably appear on Fin Raziel's face after the
battle. In a deleted scene, her face was scratched up in the battle with Bavmorda. While we do not see this in the main movie, we can infer that it happened none the less.
During the fight in the castle at the end, Bavmorda's magic turns a clear day into an overcast storm. However, in a few brief shots of the sky during the fight between Madmartigen and General Kael, the sky is blue and clear with a few white clouds.