The fact that Scout is a tomboy makes it most difficult for her to find friends of her own. Look at how she hangs onto Jem and Dill. When she needs a feminine touch she has Miss Maudie to go to, but she certainly doesn't seem to appreciate for the majority of the book her influence from either Calpurnia or Aunt Alexandra. Look at chapters 1-3 to find her displeasure with Cal, and chapter 13 and 24 to find extreme displeasure with Alexandra. This particular trait makes her quick to fight and uncomfortable around women.
Scout is naive. This trait makes it difficult for Scout to understand most situations. For example, at the jail when the mob came to mess with Tom Robinson in chapter 15, Scout had no idea how much risk she had put the children in. Fortunately it worked in her favor. This is also the case when she tries to explain Walter Cunningham's financial situation to Miss Caroline in chapter 2.
Scout seeks attention in the wrong ways sometimes. When Scout had decided to be a potty mouth, she said bad words to Atticus and Uncle Jack just trying to get a rise so she could get out of school.
Jean Louise Finch, or Scout, displays traits that will make her life hard as she grows older if she does not learn to modify them. One of the first such traits she exhibits in the novel is her belligerence. Scout is prone to getting into fistfights, using violence to solve disagreements. Obviously, this is not a trait that will serve her well in life and could, in fact, have serious consequences. Atticus is not a demanding parent. However, he does tell Scout to stop fighting, and she does her best to comply.
Another trait that Scout reveals is a know-it-all attitude. When she starts first grade, she already knows how to read, and the instruction is legitimately beneath her skill level. One has to suspect that it was not only her precocious skills but also her superior attitude that irritated Miss Caroline, her teacher. Throughout the book, Scout proudly spouts off her knowledge, even when incomplete, an activity, which, at her age is cute. However, such haughtiness can lead to one not admitting or realizing what one does not know, which can lead to problems. By the end of the book, she has softened only somewhat, declaring that she doesn't have much more to gain from school "except possibly algebra."
Scout disdains societal expectations. Although this is refreshing in that she does not harbor the racial prejudice that blights her town, it also means she does not value what it means to be a lady or to be a Finch. This creates an ongoing conflict with Aunt Alexandra, who believes that for Scout to succeed in society, she has to be able to function within its rules. Scout grows in this area when she helps Alexandra serve tea on the day they learn of Tom Robinson's death. She finally appreciates the strength required to be a lady.
Finally, Scout often lacks empathy. The reason Atticus disapproves of the children's Boo Radley games is that it shows that they do not care about Boo's feelings as a human being. Atticus sets out to teach Scout about the need to walk in another person's shoes, and by the end of the book, her ability to look at things from different perspectives has greatly improved.
Although Scout has several characteristics that will make life hard for her, she also has caring teachers and mentors in Aunt Alexandra and Atticus who help her tone down the negative side of those traits.