We have seen how a character’s physical defect or disorder becomes a powerful symbol of another deeper and more serious problem or concern. ...

In the novel, Milkman notices, by the time he's fourteen years old that "one of his legs was shorter than the other."  It affects the way he walks and the way he dances.  Despite the fact that the narrator tells us that the deformity was mostly in Milkman's head, "It bothered him and he acquired movements and habits to disguise what to him was a burning defect."  He even crosses his legs a certain way to conceal that the left leg was a half inch shorter than the right.  The "deformity," if we can even call it that with its mostly imaginary nature, goes with Milkman's tendency to feel that he is owed something, that he deserves or doesn't deserve something, that he's been a victim somehow.  The deformity with his leg is just one more example of something happening to Milkman, something he doesn't deserve, some way that he is just a victim of life.

His sister, Lena, actually calls him out on this once in the novel, accusing him of "Using [Lena, Corinthians, and their mother], ordering [them], and judging [them]."  Everything has always been about Milkman, providing for him, caring for him, doing for him, and he has grown to expect to be treated this way by everyone, all the time.  Later, in Shalimar, Milkman is hunting bobcat with some locals, and he notices that "the pain in his short leg was so great he began to limp and hobble."  He considers how much he did not "deserve [the] contempt" of the locals when he tried to buy a new car without trying to fix the old one.  In this moment, he has a stunning epiphany:

It sounded old.  Deserve.  Old and tired and beaten to death.  Deserve.  Now it seemed to him that he was always saying or thinking that he didn't deserve some bad luck, or some bad treatment from others.

Milkman had felt that he didn't deserve his family's dependence or hate, that he didn't deserve to hear his parents' terrible stories, that he didn't deserve Hagar's anger at him, and so on.  Suddenly, however, he realizes that he has thought of himself as the victim of everyone else's behaviors instead of taking responsibility for his own life and choices.  He realizes that he's only wanted others to share their happiness with him and never their pain.  Once he experiences this realization, his leg doesn't bother him any more.  When he thought of himself as a victim, the leg was one more thing he didn't deserve; when he begins to take responsibility, his "deformity" is no longer an issue.