Continuity mistake: In the US released version the scene with Meg Mucklebone (green swamp creature) was severely shortened. The problem is that one second Jack has his shield and then when he beheads Meg, the shield is hanging in a tree behind Meg. In the director's cut Meg grabs Jack's shield and uses it as a mirror.
Continuity mistake: In one shot, as the goblins are chasing after the wounded unicorn, four goblins are seen riding around a bend in a shot that presumably was taken from the first part of the film where the group was made up of four.
Continuity mistake: Brown Tom is shot in the hat by the Goblins while defending the last Unicorn. In the scene where it happens, the arrow pierces the hat right below its tip, but when he recovers consciousness, the arrow is placed in the brim.