Alexandra isn't the most likable person in To Kill a Mockingbird--only the miscreant grandson, Francis, speaks very highly of her--so it's not that surprising that Scout does not want her ultra-bossy aunt to move in with them. Alexandra invites herself to come and take care of Jem and Scout during the Tom Robinson trial. When the kids first see her, she is on the Finch porch
... sitting in a rocking chair exactly as if she had sat there every day of her life.
Alexandra faults Scout for the way she dresses and her unladylike ways, and Scout has never particularly enjoyed visiting Finch's Landing at Christmas because of Alexandra's strictness and sharp tongue. Alexandra lords her supposed superior heritage over others (which contradicts Atticus's explanation to Scout that they are common people), and Scout knows that her aunt is trying to replace Calpurnia in their household. Scout claims she can "never think of anything to say to her," and she knows that auntie thinks her "dull in the extreme because I once heard her tell Atticus that I was sluggish."
Scout refuses to tell Atticus her true feelings because
... one must lie under certain circumstances and at all times when one can't do anything about them.
Scout cannot stand living with Aunt Alexandra. Scout does not like being judged by her critical aunt and has nothing in common with her. Alexandra prefers that Scout wear dresses and act like a proper Southern Belle, but Scout would rather wear overalls and play with the boys outside. Scout and Alexandra also argue over who Scout should associate with. When Aunt Alexandra tells Scout that she cannot play with Walter Cunningham because he is trash, Scout gets upset and retaliates. Despite Scout's negative feelings towards Aunt Alexandra, she realizes that her situation is hopeless and does not argue with Atticus about living with Aunt Alexandra. As was mentioned in the previous post, Scout comments that it was necessary to lie because she couldn't do anything about it. Scout also respects her father's decisions and understands that when Atticus makes up his mind, his decisions are final.