Sounds odd. Have you checked that the bones they should have left behind didn't just merge with one of the existing bone stacks (adding to the number of bones in them)? Usually like items stack automatically, but there are cases when they do not (withes released when drying meat is one case), and there aren't that many kinds of human bone (Njerp bone is distinct from Vagabond Robber bone, which is distinct from Kaumo Robber bone. I suspect the Robber part isn't significant, but that it's only the culture that is, but I'm not in the habit of murdering civilians, so I've not been able to investigate it).
I generally lift the dead njerps/robbers up to the world map and wait until they've decayed into bone. At a convenient time thereafter I collect the bones and store them on a trophy rock out in the rapids outside my homestead (where they're out of reach of the bone nibbling dog). That, however, also means the normal stacking rules apply for my storage.