Question: Why did the two cops threaten to put Matilda in an orphanage? Matilda had nothing to do with her father's dirty dealings.
Answer: The cops are being unprofessional and rude, but they probably have experience dealing with people like Matilda's parents. They assume that she will have few options - if any - after her father goes to jail. No responsible family members who will take her into their home, etc. Depending on what Mrs. Wormwood might be charged with (being an accessory to her husband's crimes), she could also go to jail, and Matilda will need to be placed in an orphanage or foster care.
Question: Why didn't Miss Honey or any of the other teachers report Miss Trunchbull's abuse?
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.
Answer: They would have been simply too afraid of the Trunchbull to report her.
Answer: Some of the staff also appear to be on her side, as we see the lunch lady appears to hate kids too. I always found it interesting that when she is scared away at the end, we don't appear to see any other teacher cheering her away except for Miss Honey. There may have been other teachers who had a "beat them and discipline them" idea just like hers.
Answer: In the books, Matilda discovers she has the ability to do things with her mind due to her intellect.
Ssiscool ★