I know she died of old age because her hair was gray.
Another possibility is if you accidentally disturbed (possibly without noticing) the villager carrying the skeleton. In that case I don't think the deceased will appear in the graveyard, even if there is room. They should appear in the ROD, though.
By the way I always pick up the villagers when they're carrying skeletons because it's just so spooky.
Thanks for the help everyone. ~VFLover09