My routine when I find a new village is to trap all the villagers in their houses until I can build a wall and make the village safe. I wait until they're inside, then cover up the door with a couple of blocks. This time, the first time I've fixed up a new village since the expansion, I heard a lot of door noises, more than usual, but I figured it was just the changes to door sounds. But when I went to let the villagers out, the doors were open behind the blocks, and the villagers were gone. I think they tried to walk into the blocks and suffocated, but that never used to happen. This time there were only two villagers left, out of a well-populated village. It's possible that zombies were able to kill them through the corner of the blocks, but either way it seems like a bug.