Continuity mistake: When Matilda makes the chalk write the message on the blackboard, the writing changes. Watch the "Agatha," especially. The handwriting changes and the comma changes length, as well as most of the message changing. Also at the end of the message Matilda "writes" two long lines under it, which cross over. Yet later when Miss Trunchbull flies off the globe you can see there is just one line under the message, not two. (01:20:20 - 01:23:00)
Revealing mistake: As the Wormwoods are driving out of the hospital parking lot at the beginning of the movie, the shot of the car driving from right to left has been flipped, as evident by the quick appearance of a hospital directory sign in the background being mirrored. (00:01:48)
Visible crew/equipment: When The Trunchbull lifts her car back to her house and gets frightened by a black cat, a camera is reflected in her car on the left side of the screen for a moment.
Continuity mistake: When Zinnia removes the hat from Harry's head after Matilda glued it, in one shot the hat is almost removed from the forehead but in the next shot the hat is still on it.
Continuity mistake: At the end when Trunchbull throws the boy out of the window, we see when he is flying back in that the brown car is parked about 6-8 feet away from the building and bushes. When Trunchbull runs out of the building to the car after having food thrown at her, the car grill is now almost touching the bushes and the car is further from the stairs. (01:26:00 - 01:28:00)
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.