Question

What is an author's purpose in having a character not fit in or be at odds with a story's setting?

Answer 1

To show the audience that not every body acts the same. That each person has something inside of them that makes them unique. The author might also make the character not fit in because he wants the audience to see that although people live in this "perfect word" there will always be that one outsider that make a change in the "perfect world" 

Answer 2

The author's purpose is often to make a point or help readers understand settings that they may encounter in life. Having a character that does not fit in may allow the author to convey a theme by writing about the character's struggles.