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 the assistant says she smells dogs droppings, the card in her hand changes.
When Luke hides in the bowl of chips, as a mouse, the amount of chips in the bowl changes.
Before the Grand High Witch transforms at the dinner, some of the witches behind her are still women. Seconds earlier, they were transforming into rats.
As Luke lies down on the bed, the position of his drawing changes.
At 1:20.01 there is a hooded rat, not a mouse, in the scene.
Grandma's left pinkie fingertip is supposed to be missing, but it's visible in some shots.
Some of the witches in the convention are clearly men in women's clothing.
Some bald witches are obviously wearing bald caps.
The Grand High Witch's mask changes from hanging off her face to being attached as the good witch walks past, right before the other witches come to her room after drinks.
The cook says, "What's that, eh?" without moving his mouth.
When Bruno says "I really hate margarine," his mouth is out of sync.
When Mr. Stringer says, "What the devil!" his mouth doesn't move.
When Miss Irvine pours water in her glass in her hotel room, she says to herself 'I didn't want to be one of them anyway?', but her mouth doesn't move.
Near the beginning, Erica's mother says, "Come in Helga, have some cake", but she's mouthing something different.
When Luke chases the stroller that was pushed downhill, a safety cable is visible, attached to the bottom of the stroller.
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.
When Luke turns into a mouse, a character mark is visible on the floor by the Grand High Witch's feet.
When Luke is first seen training his white mice, a string pulling a toy skeleton is visible on the top left corner of the shot.
Helga's doctor tells her she cannot eat candy. Since this is set in Britain, the doctor should have said "sweets".
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 is waiting for Bruno to arrive she says to the Witches at 4:15, when he should be arriving but then changes the time to 6:15 when Bruno is in the room with them and does the count down.