This is the second time in a few weeks this has happened to me in my world. I have a temple with a nether portal at the top and underneath are cells for villagers a set up for a trading hall I was building. It had about 18 villagers at the time of the first issue. I'm not sure whether it is in the spawn chunks but certainly is within a couple hundred blocks of world spawn. Working on a project several thousand blocks away from spawn i noticed two villagers from a city I was building had disappeared. Not really thinking it may have been more than a zombie, I made my way back to the temple through the nether and found all the villagers in the hall, the iron golems, the cat the dog and the hopper minecart from the drowned farm I built from a zombie spawner had all vanished. 

Given that amount of work involved in capturing and curing all these villagers and setting up required trades this is a massive disappointment. Bad enough after a few weeks not having the heart to play from that disappointment this week I've been back curing and once again bringing in fresh villagers. Last night the last thing I did was cure a librarian and spent more than half an hour re rolling trades to get something I wanted. I logged out of the game afterwards just outside the entrance. On opening the world again today once again I've found every single villager, and the hopper minecart have once again summarily vanish and disappear on me. It is a futile exercise for me now. Why bother repairing the damage if it's going to happen again. The game is so laggy and so buggy at times it isn't worth the headache of playing since the enjoyment is being crushed by the amount of issues going on.