Revealing mistake: The two unicorns are a stallion and a mare in the movie. But both horses used were clearly stallions. This can be seen quite well when the "mare" is jumping around after she comes upon the stallion with his horn removed; a full shot of the male horse anatomy.
Revealing mistake: In the opening scene where you see the bear walking by, you next see a deer standing. The deer has a rope around its neck and is tied to something.
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.
Revealing mistake: When Blix fires a fireball at the goblin in the woods with the unicorn horn, the flame sets fire to the goblin's behind; he sits in a bucket of water to put it out but the flame goes out before he actually sits right down or the 'hiss' of steam appears.
Revealing mistake: After Lily runs into Nell's house to escape the goblins, the baby in the crib is a doll.