When Lily goes back to tell Brown Tom that Darkness has sent the goblins to find the mare, she runs behind Brown Tom very um... panic-y. It cuts to the goblins, then when it cuts back to Brown Tom, you can see Lily standing in the background on the upper left side of the screen looking pretty bored. Its only for a moment.
When Lily goes to find Jack after touching the Unicorn, her dress isn't wet. Wasn't she just kneeling in a stream of water?
Right before Lily says "I only wanted to touch one. Where's the harm in that" it shows her turning her head to face Jack. Her hair is abnormally curly in this one shot.
When Oona flies away from Gump towards the end, a black rod (part of the fx equipment) swishes above Gump's head briefly in the top right hand side of the frame.
In the snowy scene where Jack is looking for Lily, he holds up a lantern and you can see the inside of his cape. If you look closely you can see a shiny safety pin.
Both of the Unicorns are stallions. In the story they're supposed to be a mare and a stallion.
when Jack is fighting Darkness in the dungeon, there is a shot of Darkness from behind. His cape falls away and you can see a strip of white above his costume that didn't get makeup... It kinda takes away the whole moment for me. :(