Continuity mistake: When Charlie Allnut grabs a bottle of gin from the box, all the bottles in it are wrapped with paper for transport. But when Rose Sayer takes the bottles out of the box to empty them into the river, the paper is gone (from the movements of her hand/wrist, you can tell that she doesn't unwrap the paper from the bottles).
Continuity mistake: When Alice shrinks after being huge in the forest, you can see both pieces of mushroom in her hands, untouched, although she has taken a bite out of both pieces. (00:36:40)
Continuity mistake: When the Sutherland engages the four French ships, her masts are shot to doll rags, with the upper masts and fighting tops plunging to the deck. However, the lower shrouds and ratlines, which are attached to the tops, remain intact.