Plot hole: At the end of the movie, the witch's secretary returns Luke's pet mice to him even though she had no knowledge of their whereabouts or the fact that those two specific mice were his.
Suggested correction: Just before Luke and Helga leave the hotel, Helga gives Luke a tag with the address of where they live written on it. Luke took the tag and delivered it to the room where Miss Irvine was staying in. Miss Irvine is looking at the address as Luke and Helga leave the hotel. She most likely saw William and Mary at some point in the hotel and is clever enough to figure out that they're Luke's pets.
Audio problem: When Luke (as a mouse) finds Formula 86, we hear him say, "We got it, Grandma," but his mouth doesn't move.
Continuity mistake: At the end of the movie when the Grand High Witch's assistant watches Luke and his Grandma drive off from the window, she pulls the curtain and is not wearing gloves.
Other mistake: When the Grand High Witch, the Woman in Black, and the other witches are counting down the seconds for Bruno's transformation, Luke temporarily steps out from behind the screen. Yet none of the witches in the front row notice him.
Continuity mistake: When the evil witches start turning into mice, there is a close-up shot of the Woman in Black with mouse ears and whiskers, and her wig has fallen off. When the Grand High Witch is holding the spoon, there is a background shot of her dining room table, and the Woman in Black's wig is back on her head.
Continuity mistake: When Grandma says "Bruno's dad is about to have the soup", her right hand appears/disappears holding the bag depending on the shot.
Continuity mistake: After Grandma swings her closed bag in front of the Jenkins, angle cuts to a close-up of the bag and it's open.
Continuity mistake: Bruno's dad is about to have the soup and says "this is a nightmare", his wife is either holding the glass of wine or not, depending on the shot.
Continuity mistake: When Grandma says "Bruno's dad is about to have the soup" she is either holding the bag above the table, or the bag is resting on the table and her hand is gone.
Revealing mistake: When the mouse is pushing the potion down the spoon handle towards the soup, both the bottle and the spoon turn green due to the chroma screen.
