Villagers disappear after one in-game day when enclosed in an inescapable 3x2x3 area.

Villagers shouldn't disappear when enclosed in a space like described above that they cannot escape from. However, when I leave and go to a different area (on the same map) for one in-game day, then return, some of the villagers are gone. This is bad because the population decreases. This happens inside buildings and related structures.