Ah, for that you'll need to visit the NPC who is taking care of animals. If you use the fast travel system (by jumping into one of the puddles in front of a shrine), travel to the "Blue Witch" and then go one screen to the right.
Oh shoot, I really hope not. Let's see if this works: I'm attaching a map where I've put a red circle around all of the spots where you can find bones by digging up a grave. Try going back to each location and checking the graves there. If you've already dug up a grave, there will be a brown X in front of the headstone. There should be one grave in each location except for the graveyard, where there are five graves with bones (and one grave that leads underground). If you still don't have all of the bones after that, please let me know.
