Miss Honey also gets one in both the book and the film when she calls Mr. Wormwood out for considering some stupid TV show (in the book, it was a soap opera; in the movie, it was a televised boxing match) more important than his daughter.
And again when Matilda's dad makes disparaging comments about college-educated people and Miss Honey points out that educated people have a place in the world (if, Heaven forbid, Matilda's dad had a heart attack, the doctor that cared for him would have been college-educated or, if Matilda's dad was sued for selling faulty cars, his lawyer would have been college-educated).
Mr. Wormwood: What car? Sued by who? Who have you been talking to?!
Matilda gets a bit of one when she calls out her dad on his monstrous sham of a used-car-lot....and the glued-on-hat prank she plays after he berates her for calling him out.
During the two-times tables class discussion, Miss Honey explains that eventually they'd be able to multiply any numbers, whether it was 2 x 7 which the class answers correctly as 14, or 13 x 379, which most of the class is amused by, but Matilda, in about one second, answers 4927, shocking everyone, especially after Miss Honey multiplies it by hand and determines she was correct.
It's even more awesome when Trunchbull smashes the glass platter over his head. While that is a bad thing to do to a kid it gives two more awesome points for Bruce: 1. Being that he is durable enough to take a heavy glass platter over the head with nothing short of a loud belch. 2. It gives Bruce the satisfaction that the aforementioned action meant he got to Trunchbull showing us a glimpse of her Villainous Breakdown.
Similarly, Matilda, followed by her fellow students, standing up and cheering for Bruce when he shows signs of giving up, continuing to support him even as the Trunchbull screams for quiet. It's their encouragement that give Bruce the strength he needs to polish off the whole cake, even licking the platter!
Miss Honey also gets a slight one when she finally stands up to the Trunchbull.
Miss Honey: I am not seven years old anymore, Aunt Trunchbull!
Trunchbull really chewing out Harry Wormwood over the car he sold her at the start of her house rampage. note "....shove it up your bazooka!", indeed!
The Feds likely got this when they nailed the Wormwoods in Guam.
The end of the film version of Matilda features this scene at the end when Matilda's family is forced to leave the country.:
Matilda: I love it here! I love my school; it isn't fair! Miss Honey, please don't let them...
Harry Wormwood: [interrupting] Get in the car, Melinda!
Harry Wormwood: Whatever!
Matilda: I want to stay with Miss Honey!
Zinnia Wormwood: Miss Honey doesn't want you! Why would she want some snotty, disobedient kid?
Miss Honey: *sincerely* Because she's a spectacularly wonderful child, and I love her!
Doubles as a Crowning Moment of Funny, but:
Matilda: Here, I've got the adoption papers right here!
Zinnia Wormwood: Where did you get those?
Matilda: [Gives her a triumphant look] From the library! I've had them since I was old enough to xerox!
Miss Honey's method of teaching eight year old children to spell "difficulty" is pretty cool.
Mrs D. Mrs I. Mrs FFI.
Mrs C. Mrs U. Mrs LTY.
In the scene before the scene with Trunchbull's comeuppance....Matilda goes to Trunchbull's house and uses her telekinesis to simulate a haunting. Among the chaos; Ms. Trunchbull's portrait (of her as an Olympic athlete standing on the field with a javelin) flies off the mantle into the fireplace (and gets burned to ash) and the portrait of Magnus flies down the stairs and takes it's rightful place on the mantle!
In the movie, the Trunchbull ends up lying in the hallway after failing to take control of Miss Honey's class; all of the children from that class throw their lunches at her while the other children of the school watch. When the Trunchbull finally gets up and turns around, she sees every single student in the school—all of the kids she's terrorized and bullied for years—standing silently, armed with their lunches, along with toilet paper and water balloons. They proceed to absolutely pummel her, sending her running from the school humiliated and embarrassed. It's the perfect revenge for the cruelty she's inflicted on them.
In an awesome Brick Joke, Bruce Bogtrotter, whose actions are described above, is among the students who take down the Trunchbull with their lunches. What does he do? He marches right up to the Trunchbull and smears chocolate cake across her mouth!
"The School Song" sequence where two dancers would climb on the school gates as alphabet blocks are inserted through the holes and they adeptly climb on them on lyrical cue.
Matilda's class standing up to the Trunchbull by misspelling words.
Matilda rallying the students to cover up the Trunchbull's latest victim with their coats, then telling the headmistress that the boy suffers from narcolepsy, and therefore couldn't be guilty of the (imagined) crime. Not only does this show Matilda using her cleverness to help others, but the fact that the rest of the kids are willing to go along with the charade foreshadows the "strength in numbers" message of the musical as a whole.
Matilda standing up to Ms. Trunchbull during gym class when she starts tormenting a young boy.