When Alice is fanning herself, and she starts to shrink, she says "What's happening now?" but her mouth doesn't match up with the lines.
Right after Tweedledee and Tweedledum finish the Walrus & Carpenter song, a crew member runs into the shot, turns and runs back out really fast on the left side.
When the Jabberwocky is flying, we see a close-up of him with a wire visible on his back.
When Alice first leans on the Caterpillar's mushroom, it bends to show it's a mattress.
A portrait of Queen Victoria on the wall of Alice's house implies that the movie has an English setting just like the book, yet the family has American accents.
When Alice grows tall in the hall of doors, the Rabbit's gloves are on the table, but this is before she sets them there.
The scene right after the White Queen turns into a goat and Alice runs off to another part of the woods, she sees a giant black bird chasing her. In the shots of the bird chasing Alice, there is wide open land, but in other scenes Alice is in the forest.
The Jabberwocky, during the palace party crashing, flies but its wings never once flapped.
The ending credits of both parts say (in order of appearance). In the Looking Glass Land half, the movie starts with the Jabberwocky in Alice's house going after Alice, but the credits have the Jabberwocky placed after Humpty Dumpty. The Jabberwocky should have been the first in the credits as it's an order of appearance format.
In the Looking Glass Land half, Alice and the Red Queen walk onto a chessboard with a house on the left and a castle in the distance. Later on, they run through the woods and into another wide-open land of another chessboard. In between shots shows both chessboards which are very different from each other.