1. Stubbornness. How many times in the story did Jem insist that she stay put and she absolutely refused? This got her into trouble over and over again, and made her life harder. However, hopefully as she matures, she will be stubborn about the right things, like Atticus is, and it will end up being to her credit.
2. Tomboyishness. She will eventually, as she admits at the missionary circle, have to "soon enter this world", meaning the world of a lady. She fights it though, and as a result earns people's scorn and judgment, including many townfolk and Aunt Alexandra. Later this could be hard for her as she tries to fit in with girls her age, as Jem eventually moves out of her sphere of friendship. It will be a rough transition for her, but hopefully she can make it with few hiccups.
3. Always speaking what is on her mind, with no regard for social tact. We see Scout do this many times throughout the book, blurt out questions, judgments, perspectives and attitudes without even thinking beforehand whether it's the right time or place. This gets her into awkward and troublesome sitiuations, and could potentially earn her enemies in the future, when people can't pass it off because she is young. However, it is what gives her much of her charm in the book, and I find her forthrightness refreshing. :)
Scout's character was one to always question things. She didn't seem to understand the injustices of her world, and she doesn't accept them. Leading up into her adult life (in the 60's), she would have a hard time with the Civil Rights Movement. Even though she believes in people, not colors, she would face hardship with that point of view. Too many people were obsessed with black and white, rather than who was underneath.
She was a very outspoken little girl, too. She was always the one to tell the teacher the way "things are" or to attack a grown man she didn't know who was most likely holding a shotgun. (that was in front of the jail house) Unfortunately, she would not be able to really speak her mind as a women until far into her old age. This too would make trouble for her later in life.
One of her other traits was that she was so impetuous (hot-headed) about everything. The first thing she answered with was her fists. Although later she begins to follow Atticus' model of behavior, it is a characteristic of hers that would immediately get her in trouble later in life. We can't answer all of our frustrations by punching someone else.