Fort Wagner's massed graves were not really unique. The unhonorable treatment of bodies was common throughout the war on both sides. Most would be lucky to be buried deep enough that the rain wouldn't was them up, or that the bodies still had clothes on or simply wrapped in a blanket. A great many bodies were naked, or stomped on and pressed into the pile to make more fit into the hole. Confederates were not givin much honor by their Northern counterparts in burial, at Gettysburg many were tossed (not placed), bursting swollen bodies open, into large shallow holes and some dirt thrown on top.
Shaw is lucky he was not captured or he may have suffered a worst fate than being buried in a massed grave, see the Battle of Milliken's Bend, LA.
There is also some differences of the story on Shaw's burial. This from the O.R. Page 463, Series 1 - Volume 35 (Part I)
"They state that Colonel Shaw, Fifty-fourth Massachusetts, was killed on the parapet, but there is difference of opinion as to where he was buried. They state that the colored soldiers who were captured were treated as prisoners of war, the same as the white soldiers.
I remain, very respectfully, your obedient servant,
W. W. H. DAVIS,
Colonel 104th Pennsylvania Volunteers, Comdg. Post. [to Headquarters U.S. Forces Morris Island, January 31st 1864"
___________________________
David Upton