Continuity mistake: While with the Dodo Alice sees the rabbit arriving ashore next to a stone. A shot later the stone disappears.
Continuity mistake: When Tweedle Dee and Tweedle Dum show up, the tree where Alice looks if the rabbit is hiding has a huge bush on the right that disappears a shot later.
Continuity mistake: When Alice arrives at the shore where the Dodo is her hair gets soaking wet when the waves crash on her, but the second time this happens her hair is dry and perfectly brushed and remains this way for the rest of the scene.
Continuity mistake: When Alice arrives ashore where the Dodo is and fish step on her head three stones behind her suddenly appear between shots.
Continuity mistake: The box with the 'Eat me' cookies suddenly disappears a shot later.
Continuity mistake: The cork that Alice leaves on the table disappears in the following shot only to reappear later on.
Continuity mistake: The 'Drink Me' text on the label disappears when Alice drops the label.
Deliberate mistake: Rocks on the water suddenly appear when the rabbit shows up, which allow for Alice to chase him.
Continuity mistake: When Alice lies by the brook the shore is really short, and it makes a turn to the right where a big rock is. When the rabbit appears the rock is gone and the shore is really long, with cattails everywhere.
Continuity mistake: When the rabbit first appears there's a close-up on the kitten and Alice's dress disappears from behind.
Continuity mistake: By the brook the distance between Alice's hand and the kitten's paw increases between shots.
Continuity mistake: Sitting on the tree Alice says she would make a world of nonsense and the cat's fur swaps from light grey to light yellow.
Continuity mistake: When the movie begins Alice's sister has a lot of tree trunk above her head, but a shot later Alice is right above her, with her skirt touching her sister's hat.
Continuity mistake: When Alice arrives at the rabbit's house a watering can appears on the right. Also, the fence runs straight in the wide shots, but a door in between two rabbit sculptures appears in the close-up.
Continuity mistake: When Tweedle Dee and Tweedle Dum show up Alice says "do you think he should be hiding?" and the flowers on the grass next to the tree disappear.
Continuity mistake: The way Alice holds the 'Drink Me' tag differs between the wide and close-up shot.
Continuity mistake: When the movie begins, Alice says "Nonsense" and sits the cat on the white part of her skirt. Wen the shot changes the skirt is blue. Then the angle changes and the skirt goes back to white.
Continuity mistake: After shrinking, a box appears on the floor between Alice's legs. She opens the box and takes out a cake. In the next shot, the box has disappeared.
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