Capt. Henry Wirz, commander of Fort Sumter (Andersonville) POW camp was tried, convicted, and hanged for violating the rules of war in his treatment of Union prisoners at the camp. The specific charges included "violation of the laws of war, to impair and injure the health and to destroy the lives—by subjecting to torture and great suffering; by confining in unhealthy and unwholesome quarters; by exposing to the inclemency of winter and to the dews and burning sun of summer; by compelling the use of impure water; and by furnishing insufficient and unwholesome food—of large numbers of Federal prisoners."
The Andersonville National Historical Site contains the National POW Museum. They would probably be the best source of information about prosecutions for mistreatment of POWs during the Civil War.