Continuity mistake: Alice's necklace keeps disappearing and reappearing after falling down the rabbit hole.
Deliberate mistake: When Alice jumps on the dog and they start running, her dress and her hand-band suddenly changed side. Probably they mirrored the image, and instead of going left as directed, it felt more accurate to go right.
Continuity mistake: In the Red Queen's courtyard after small Alice trip with Bayard, the Rabbit gives Alice an upelkuchen cake to grow. When she starts growing you can see she has a smudge of cake above her lips, but after the change in shot, it is gone.
Continuity mistake: During the execution scene, the executioner moves the ribbons of the hat "to see better" but when the angle changes the ribbons are where they were before.
Continuity mistake: In the beginning of the film when Alice is laying in bed her father shows her how to wake up from a dream by pinching herself. He demonstrates by pinching her upper arm on the bicep. Switch camera angle and he is pinching her on the shoulder, when the camera switches back he is once again pinching her arm.
Continuity mistake: When Alice first sees the tiny door (having just dropped into the rabbit hole) the keyhole is on the left-hand side of the door, but when she later uses the key to open the door she puts it in the right-hand side.
Revealing mistake: In a close-up, just after the defeat of the Jabberwocky, the White Queen collects the Jabberwocky's blood dripping from its teeth into a vial. Cut to a wider shot with the vial just over half full, you can see that the drips are still being caught by the vial (ie, they don't drop past it onto the ground), but the level of blood in the vial doesn't rise, revealing that it is done in post-production.
Continuity mistake: When the red queen is sitting in her chair and she is talking with Ilosovic Stayn, her lipstick is heart shaped. But when the camera switches to the side, her lips are fully covered in red and when it switches back it is heart shaped again.