These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Broken Aesop: The entire premise of the novel is that looks can be deceiving- the beautiful Sophie is selfish, and the ugly Agatha is goodhearted. But at the end, Agatha becomes incredibly beautiful and Sophie becomes ugly...so their morality does match their appearance after all.
The fearless Agatha is chosen to become a princess! Surely this means that the in-universe stereoypes about princesses always being frail and meek are false...right? Actually, no- when things get dangerous, Agatha is quickly and inexplicably reduced to a fearful victim who can't defend herself against Sophie.
Darker and Edgier: The second book might as well be titled "Well, That Escalated Fast".
Designated Hero: In one scene, Tedros (the story's Prince Charming) literally kicks a bunny. And yet the protagonists spend the whole book competing for his affection and listening to Tedros whine about how nobody really understands him.
Family-Unfriendly Aesop: The second book boils down to saying you can't love both a romantic interest and a friend, you have to choose one or the other.
Ho Yay: Tedros kisses Sophie...as she's disguised as a boy, and Tedros fully believes she's a boy.
Informed Friendship: In theory, Agatha considers Sophie's friendship so important that she would risk her life to save Sophie, and reject the School's norms for her. In practice, both admit (in the first chapter, no less!) that Sophie only spends time with Agatha so she will have a better chance of being declared a Princess. Both before and after this, their relationship is marked by lying, insults, and Sophie's attempts to mold Agatha into the obedient friend she wants.
Les Yay: Between Sophie and Agatha. It eventually blossoms into full on Foe Yay as Sophie accepts her role as a witch, and Agatha hers as a Princess, only to return to Les Yay as Sophie sacrifices herself to save Agatha, and the two are reunited and returned home.
Moral Event Horizon: Sophie first crosses this when she murders The Beast for cutting her hair. She does it again when she breaks her promise to Agatha to arrange to kiss Tedros, in favor of wanting to stay and try to become a Princess. She crosses it a final time when she arranges for Tedros to find Agatha, whom he loves, in her arms at the Evil Ball. Of course, how much of this was of her own volition is questionable as it's implied that some, if not all of her Evil behavior may be due to the Head Master's control of The Storian.
Villain Sue: Sophie is often shown to be incompetent at magic, both compared to Agatha and the other Evil students. Yet, when the plot requires her to do villainous things, she's suddenly slinging spells with the best of them.
The Woobie: Dot. As a villain, she's got her work cut out for her. Her talent is turning things into chocolate. She gets kicked out of her room by Sophie, Hester, and Anadil. And even Agatha pulls her hair when she learns that Dot knows how Sophie and co. have been entering the school and defacing it.