In Alice's final singing scene, in between shots her hair changes from being behind her shoulders on both sides to being in front on one side.
When Alice is enlarged from the bottle, her arm keeps changing from halfway out the window to her entire arm out the window.
Major Caterpillar said that one side of the mushroom makes you smaller and the other side makes you larger.
Initially, Alice takes a bite from the piece in her left pocket and it makes her larger.
During the hearing she takes a bite from the piece in her right pocket.
It should have made her smaller, but it makes her larger.
During her visit with the White Knight, footage of Alice nodding is used twice.
When the Queen of Hearts decides to decapitate the cards who were painting the roses red, Alice hides them in her skirt to save them. However, they are never seen getting out, and no further reference is made to them in the film.
The Mad Hatter knows Alice's name without being told what it is. This may have been deliberately included to suggest that he is part of Alice's subconscious.
When Alice first shrinks, a (relative to her) gigantic bottle hits the ground next to her and she doesn't jump, she doesn't so much as flinch.