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.
While Tedros/Agatha is liked well enough, there are many Sophie/Agatha fans who were disappointed that not only did the girls not become romantically involved but turned out to be sisters Separated at Birth.
Tedros kisses Sophie...as she's disguised as a boy, and Tedros fully believes she's a boy.
A female example is 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. Then it's subverted when they turn out to be sisters.
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.
Sequelitis: The second and third books weren't as well-received as the first, particularly involving Sophie's character and the perceived Family-Unfriendly Aesop listed above.
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.