Something I enjoy about Tamora Pierce's Circle of Magic series is that the children have real, normal flaws, and are never blamed for having them, only gently corrected over time and with experience.
Sandry doesn't have that many, she's very open minded, but has some flaws in her teens. But the other three have flaws and prejudices when they arrive at Winding Circle.
Briar is slightly sexist. He protests at living with girls, and doesn't really believe they are much use in a fight until later. He complains about female stereotypes that don't really apply, such as the girls sticking their noses into his business, talking excessively, or being weepy and emotional.
Daja is xenophobic to anyone who isn't a Trader. She openly calls people a slur, even Sandry in the beginning. It takes some time to accept others not of her people as her family. She still carries that orginal xenophobia a long ways, though.
Tris is very prejudiced, she was raised that way. She is horrified to share a house with a Trader, a noble and a former street rat. Several times in the books she disparaged people she thought as lesser, such as the poor and Traders. In Briar's Book she calls street kids animals, and blames the poor for the pox.
None of these traits are super obvious, and they aren't called out right away. They are also perfectly normal prejudices and problems for children to have, especially those raised by prejudiced adults. The books doesn't encourage you to hate these children for it, nor do the kids change right away. It's a slow process fueled by their teachers and their experiences, as well as each other.
It's really great for children to read the book, recognize some flaws they have, and work through them as the characters do. And it's done mostly subconsciously too. It's a sensitive topic that is very well done.
