When the Grand High Witch and her assistant enter her room while Luke gets the formula, they're wearing pointy shoes. Earlier, it was mentioned that witches never wear pointy shoes. However, the original book suggest the Grand High Witch does wear pointed shoes to great discomfort and hates wearing them, this fact is not mentioned in the movie to explain the shoes.
When the Grand High Witch announces that another meeting will take place next year, her assistant is heading toward the exit. In the next scene, (at around 26 mins) her assistant is heading toward the same exit, from a different direction.
When Luke is playing in his tree house, the witch in black catches his fallen toy airplane. When she throws the plane back up to the tree house, a string is attached to the front of the plane, pulling it into the branches.