Okay so I successfully duplicated this bug for a few times. If you shut down the game when you are seeing a bunch of villagers, and perhaps right before some "save" functions are called, the villagers will disappear when you re-enter the game. Is this possibly an exception-handler bug or a garbage collector bug? 

This phenomenon is especially common in a world where cheating is not enabled. Every time in survival mode I fly to a new village with Elytra, see some villagers, and shut down the game (either immediately or not), the villagers disappear. But in creative mode, such chance is much smaller. 

This is a real issue because now if you don't press "save and exit" and the game reloads, then the villagers and animals will disappear. I remember the first time when all my villagers disappear is because I was changing the brightness, and when I came back to the game, it auto-reloaded, and all villagers disappeared. 

In sum, the bug is: if you don't press "save and exit" and the game reloads for some reason, you will lose the villagers (in a cheating-disabled world). 

• https://bugs.mojang.com/secure/AddComment!default.jspa?id=470207