I have a box underground that i use to keep villagers in. It is lit up and I am in the area often. Some times when I go to see the villagers a few but not all of them have disappeared. They are not free to get out and their aren't any place for them to escape. I have made sure that no zombies are able to get in so the only reason for this to happen would be if they had despawned although on the internet it says that they aren't suppose to. Also my minecart with hoppers disappear for some reason.