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.
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.
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