Amy Yvette Garrou, College admissions expert (US and international colleges)
I second Michael's advice. I would like to expand on his point about the effect of recommendations. As a college counselor in high schools for the last 12 years, I had to write a letter of recommendation for every student who applied to college. And I read all the teacher recommendations written for each student (usually two teachers' letters per student). I can tell you that it's very difficult for a teacher or a counselor to describe a student at his best, when that student's behavior isn't good. "Behavior" encompasses a lot, but here are some examples of behavior which influence a student's reputation: talking rudely to a teacher or another student in class; being part of a small-group project but not doing any of the work; always talking while the teacher is talking; coming in late all the time; and being disruptive in some other way. Most teachers have planned their classes carefully, and feel pressure to help students learn a large amount of material. So students who behave badly in class can affect the outcome not only for the teacher, but for fellow students.
A letter of recommendation for college needs to focus on you at your best. Yale and similar colleges get more than 30,000 applications per year; Yale offers admission to some 7%. So a teacher's or counselor's letter has to say more than "XX makes excellent grades." In order for that letter of recommendation to have an impact as admission officers read your file, the teacher needs to be able to say that you not only have the top grades in the class but you also raise questions that advance the discussion; that you were an invaluable part of your small-group project, and cite the work you did; that you allow others to speak even if you always know the answer. You want your teachers to think of positive examples when you ask for a recommendation. You don't want a recommender's first thoughts of you to be negative. And because the norm is usually that students are well-behaved, the students with uncooperative or disruptive behavior stand out.
It's about your reputation: not just your purely academic reputation, but about how you treat other people. Colleges are communities where students live in dormitories or apartments close together. Admissions officers will prefer to admit students who seem to get along with others, and have a positive effect on others.
I realize that "behavior that's not great" could be a range of things; it could be defined differently depending on the culture where you live. But it sounds as though you, and others, perceive that your school behavior is lacking. I would encourage you to ask teachers, other school staff, or even your friends what you can do to improve your reputation at school. When you apply to college, you'll apply to more than one (not just to Yale). Being your best self is important for all your college applications.