After Josie's nurse uniform inflates like a balloon and explodes, it shows no sign of tearing or other damage.
During the nurse disguise scene, Melody's mustache disappears and later reappears.
The Nautilus approaches the stern of the victim ship, yet Nemo's on-board screens and periscope clearly show the bow.
After they escaped from the tubes left on the ocean floor, Josie and friends should have been crushed to death by the water pressure.
In the last scene, Alexander's head is drawn on Alan's body.
During the final boat chase, Valerie appears Caucasian in a few shots.