Bad Boys: Public Schools in the Making of Black Masculinity by Ann Arnett Ferguson is an excellent analysis of the ways in which black boys are singled out and stigmatized in desegregated public schools.
Bad Boys is based on three years of field work at an school in California in the 90s, and the insights I'm sure are no less true today. Teachers and administrators, black and white, respond to these boys through the lens of racism, and these boys come to school with comportment styles formed in the face of our cultures racism. The institution of the school rewards those students who most conform to white middle class standards, and those who are routinely punished are denied school resources and put in an institutional cycle that leaves them behind academically. Looming large over them is the specter of the juvenile justice system and the criminal justice system, and Ferguson's book offers some explanation for the disproportionate numbers of black men in our jails.