I've seen some oddities with loading - particularly if waiting for the game to reload after death. I had a repeatable issue with this a while back, (and I can't remember which location this was), where there were dead mages lying on the ground as a part of a vanilla quest. There were bottles of magicka placed next to them. I picked a couple of these bottles up, and then promptly died at the hands of an enemy around the corner. When the game reloaded, to a point from before I'd picked up these bottles of magicka, when I reached the mages, the bottles were not there. If I quit the game completely and loaded the same save from the menu, the bottles would still be there. This was repeatable - if I died again and it reloaded, the bottles wouldn't be there - but if I quit the game and loaded the same save from the menu, they would be there.
Something must still be happening which doesn't refresh things completely.