Villagers on beds surrounded by solid walls get seem to "teleport" into the walls when they wake up. They nearly always suffocate and die, rarely they end up on the other side of the wall and survive.

I tested different setups and managed to prevent this issue by removing all the blocks on the level above the beds. When doing this, the villagers just bounce on top of their beds when they get up.

Glass panes also cause the villager to teleport inside the wall, with the difference that they do not die. Villagers stuck in a wall cannot move, but they will teleport into a nearby bed to sleep at night.