Consider what you have learned from Scout's interactions with Atticus, Walter, Calpurnia, and Miss Caroline.
Scout, like her father, does not see why injustice in any form is tolerated. She is able to read before she attends school and is confused as to why this is 'wrong'. Similarly, she cannot see why Walter's manners are different from hers, or that she is regarded with suspicion when she attends Calpurnia's church. Scout also cannot see why she shouldn't dress or act like a boy.
Scout stubbornly refuses to accept difference - it makes her life hard, but as we empathise with her, we understand Harper Lee's message more clearly.
The behavior that will make life difficult for Scout is her total unwillingness to follow the traditional role of the "southern female." That in a sense is part of Aunt Alexandra's concern for her. Consider the roots of Scout's reading experience with Atticus. She reads the news; she educates herself about matters that really don't "concern" females. She runs with the boys; she plays with the boys. All of her actions are contrary to what is expected of the "southern female."
I would say the character trait most likely to make Scout's life more difficult is her stubbornness. She often refuses to see another perspective and frequently becomes angry when the other person does not see her side. Although Atticus teaches his children great values, they are different from the social norm. Scout's stubborn nature makes it difficult for her to express her differing views in a polite manner. She is firmly rooted in the belief that her way is right, even with the little things like table manners. Her stubborn nature makes it difficult for her to understand that Walter's table manners are different and that pointing it out to him is rude. Of course, this stubborn nature can become as positive thing as Scout grows up. It may be more difficult for her to change, but as she matures she will begin to use her stubbornness to promote social change.
Scout clearly shows that she is a very impatient young girl with those that she considers to not display intelligence. Likewise she has a bit of a temper to her which gets her into trouble. With such a father as Atticus, and considering the way that she and her brother are brought up, where they are encouraged to question, it is hardly surprising that Scout turns her attentions to those around her and often finds various characters and situations wanting from her own perspective.
Scout's curiosity surrounding people, their similarities and their differences is an impediment when mixed with the qualities mentioned above. She wants to know why Walter has such different table manners to herself. She is confused as to why Miss Caroline objects to being questioned and is unable to explain things as clearly and eloquently as Atticus. She sees the value in the lessons she learns from Calpurnia and appreciates the experience of attending Calpurnia's church, though not all of the adults see the value in this.
Like many gifted children, and also because she has such a rational father, Scout has little patience with people who are illogical such as the one-dimensional Miss Caroline, who mistakenly considers herself educated.
Later on in the narrative, however, Scout does alter her perspective as she remarks, "Folks are just folks." And, like her father, she learns to find some redeeming quality in all but the worst.
I think that Scout's major problem is that she isn't very tolerant of people whom she thinks are fools. You can see this right away when she starts school. She doesn't really know how to politely give in to people when she thinks they are wrong. She is the type who is likely to go through life correcting other people and arguing with them even when it really isn't necessary to do so. That is not a good recipe for being popular.
We have already learned that Scout has a hot temper who is frequently at odds with adult authority. She doesn't always get along with Calpurnia, whose
... battles were epic and one-sided. Calpurnia always won, mainly because Atticus always took her side.
Although Scout seems to like Dill from the start, she antagonizes Jem until he takes the dare to run up and touch the Radley house. She speaks her mind during Miss Caroline's class on the first day of school, and she immediately gets off on the wrong foot and into trouble with her teacher. She takes out her frustrations by fighting Walter on the playground during their lunch break, and then she gets into more trouble with Calpurnia when they return home to eat. After the second half of the first day gets no better for her, she tells Atticus that night that she wants to quit school.
Scout doesn't seem to get along with the other children (aside from her new friend, Dill) any better than she does with the adults. Her independent streak is one that must eventually be tempered if she is to succeed in future relationships. And she must learn to control her anger--and her urge to settle disagreements with her fists--before she encounters a situation in which her tactics will not work.