It is rare for a bug to happen, the only two I have seen are in the Brotherhoof Safehouse. Once when a patch was installed the safehouse reset, but only the things left in the open disappeared. Also a deathclaw followed me all the way down the sewer once. Otherwise the most unsafe thing is leaving you gear as the Ranger and Legionaire will steal it.
The 'Deathclaw Incident' is a side-effect of their Aggressiveness level being through the roof, they will pursue you no matter what you do while trying to get away.
As for NPCs taking stuff, their AI routines have an 'eat' section whereby they grab the nearest food or drink item and consume it, regardless of what it is. AFAIK they will not take non-edibles; however, I don't use any of the safe-houses as a base, nor do I return there to see if any of the stuff lying on the shelves has disappeared after taking those items I actually want.
One notable exception is in the Followers' safe-house: the doc who lives there will restock the fridge daily if she's there, and when this happens anything stored therein will be summarily deleted.