Audio problem: At the end, when the Wormwoods are leaving on a permanent vacation, Harry says, "Get in the car Melinda." Matilda corrects him and Harry says, "Whatever," but his mouth does not move.
Audio problem: When Zinnia combs back Harry's hair with the grey stuff in it, we see her lips moving, but we hear Michael's voice.
Answer: The "real world" answer is that it's a movie, and without Trunchbull, there's no villain at the school for Matilda to battle. Within the context of the film, everyone, including the staff, is afraid of her and fear if they speak up, she'll retaliate.