I have a carrot and potato farm on my map and the villagers who are working just suddenly disappear.  I've lit up the area,  given them beds,  name tagged them,  traded with them, everything.  They always disappear without fail.  They have no way to suffocate and theres no way for mobs to get in.  The wall is 3 blocks high (They can jump but theres nothing to jump onto),  I put their composter above the water block and put a fence over it with a log on top of that so they're unable to jump up and suffocate.