If I may jump in here, at the Shiloh Battlefield National Cemetery there are a few Confederate burials. Of course, the vast majority of Confederate dead are buried in large burial trenches or mass graves. As I recall, the Confederates buried in the National Cemetery were soldiers who had been captured and treated by Union doctors near or within the confines of the site of the current cemetery. Rather than relocate them to a separate area, apparently, they just left or placed them in the National Cemetery. As I'm writing this, I've just done a quick search and found this in an old park brochure, "Only two Confederates are buried in the (Shiloh) cemetery. Both died while being held as prisoners of war."