As I was playing I noticed random NPCs were disappearing. I didn't give it much thought but there weren't any random attacks as I was too low of a level for the dragon born or dawngaurd quests to start.
After playing around with vanilla, I started noticing NPCs in whiterun may get stuck under the paths at the market. Its pretty random and I've caught it a few times when making a brand new character each time.
Another thing I picked up on us sometimes they'll spawn in the air. They don't fall until they move or I get close to them.
Anyhow, I'll try to provide screenshots but its pretty random.