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 Alice returns to the caterpillar and he says "keep your temper" he is coloured opposite to how he normally looks, with a dark blue front and light blue back. (00:34:15)
Continuity mistake: When the Mad Hatter grabs the White Rabbit's watch to fix it, the watch's chain has a t-bar at its end, but while the watch goes bonkers the t-bar is gone and in its place are three small keys in these shots. The t-bar reappears on the chain when the March Hare slams it with a mallet. Also, the number of links on the chain repeatedly changes between approximately eight and eighteen, quite a difference. Additionally, the direction that the watch's hinged front cover opens repeatedly changes; the hinge is at its left, at its bottom, or at its top by the crown. (00:47:55)
Revealing mistake: When Alice tells the Mad Hatter how she appeared in Wonderland the hare's paw is superimposed on the teapot's handle as if the pot were flat or he was floating.
Continuity mistake: When Alice becomes a giant she slams her right foot on the door. A shot later she is lifting her left foot.
Continuity mistake: When being a giant inside the house, Alice extends her arms and they're quite short. A couple of shots later she remains the same size but her arms are now 5 times longer to allow for her to open the windows on the front. This has nothing to do with the magical cookies.
Continuity mistake: After Alice's foot bursts through the rabbit's house, he moans and growls and suddenly disappears a shot later.
Continuity mistake: When the King smashes the Queen's crown with a hammer, it has 5 half-arches. A shot later it has 6.
Continuity mistake: When Alice eats the cookie in the rabbit's place her foot grows huge along the stairs, down to the entrance and out to the garden without knocking a single object except the poor rabbit. When the angle changes to a shot outside the house suddenly all of the furniture has magically appeared out of nowhere next to the shoe.
Continuity mistake: While sitting on the branch Alice's cat suddenly disappears only to reappear in the following shot. A shot later, Alice sits down and she reaches for the cat who is at arm's length.
Continuity mistake: After the broom-dog deletes the red road a huge rock suddenly appears in front of Alice.
Chosen answer: There is no real answer. It is intended to be left unknown. See http://www.straightdope.com/classics/a5_266.html for The Straight Dope's answer.
Guy