Roster of the Dead.
There is also at least one event when villager(s) can be killed but not appear on the ROD; it's the tsunami. Presumably the villager is dragged out to sea so is counted as 'lost' rather than 'killed'.
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.