As you pointed out, Aunt Alexandra has serious problems with the way that Scout dresses. Scout says that, in fact, "Aunt Alexandra was fanatical on the subject of [her] attire.

But she is also very concerned about the way that Scout speaks, particularly since she tends to swear when she gets very excited or angry. She also finds herself upset when she sees Scout scratch her head, this is not lady-like and therefore certainly not something to be done when anyone else can see.

Another has to do with the way that Scout does not take on airs the way that Aunt Alexandra believes that she should. Aunt Alexandra believes quite strongly that the Finches are somewhat elevated above other people in Maycomb and as such should act differently. Running around playing in her boyish clothes is just not an acceptable way for a lady of Scout's background to behave.

Along those lines, one more specific behavior that Aunt Alexandra does not approve of is Scout going to Calpurnia's church or her home. She simply does not think it is acceptable for Scout to go to a church where the congregation is black or to the home of a black person, no matter how beloved to the family.