In Harper Lee's To Kill a Mockingbird, Atticus displeases Aunt Alexandra in several ways.
It seems obvious that Atticus' sister believes the children are not being brought up properly. For one thing, Scout dresses and behaves like a boy. Atticus does not seem to mind. Soon after arriving to stay for an extended visit, Alexandra suggests that Calpurnia, as a black woman, is not the best person to raise her niece and nephew. Atticus will hear nothing against Calpurnia, citing the fact that she has been with them for years, is as "tough" on the kids as a parent would be, and is one of the family. The children love her and Atticus will not change his mind.
Related to this is Aunt Alexandra's displeasure that the children have been allowed to attend Calpurnia's church. When Scout speaks of visiting Calpurnia at her home one day, Alexandra outright forbids it, and Scout is very disrespectful. Scout is scolded by her father for her improper conduct, but Atticus does not see Calpurnia as a black woman, but as the woman who has cared for his children as if they were her own.
Aunt Alexandra is also very unhappy with Atticus because the children are not familiar with their "roots." She wants them to know the important position they are heir to in that their ancestors settled Finch's Landing, and their "elevated" social position in Maycomb County. She wants Atticus to familiarize them with the people from which they are descended. Aunt Alexandra also does not appreciate the children's knowledge of their crazy relative (Cousin Joshua) who tried to shoot the president. Atticus tries to convey Alexandra's message with regard to their social responsibilities, but it is very upsetting to Scout because Atticus does not sound like the Atticus they know, and it must also upset Atticus, for he tells Jem and Scout to forget he said anything at all.