Well, since you have the graveyard and 6 hours isn't enough time for her to have *ahem* decomposed, then she probably fell victim to one of the bugs/idiosyncrasies of v1.0. Another possibility is that you might have accidentally interrupted a villager who was carrying her to the graveyard. When that happens, the villager 'drops' the bones (sort of like they do with food or building materials when you interrupt them) and they don't make it to the graveyard.

By the way, the flowers were left in the graveyard by a villager who was honoring the dead. They fade away after a short time.