Continuity mistake: When Matilda's family is speaking out numbers and summing them up, the mum places a can of beer on the table that moves around between shots.
Continuity mistake: On Matilda's first day of school she gets off the car wearing a sweater and holding a notebook but them is shown just wearing her blue dress.
Visible crew/equipment: When Matilda makes the pitcher fly up in the air you can see the shadow of the stick that was later deleted and erased.
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.
Character mistake: When Harry takes the kids to his business, he's showing them how he "restores" cars. After putting the bumper on, Harry says, "Transmission. The sawdust quietens the gears and let's the engine run as sweet as a nut." Putting sawdust into the transmission would not change how the engine runs as they are two separate components. It may make the transmission quieter but would have zero effect on the engine.
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.