Had a pen with several villagers in it. It is both mob spawn proof and have plenty of room for them to move. It has happened twice now that all the villagers in this pen have disappeared without a trace or reason. Not only is it mod spawn proof and made with blocks so there is no chance for them to get hit but I am standing too far for mobs to spawn (AFK playing). The other such pens I have made do not seem to have this issue even though they are identical.
It may be related, my horses often load out of the fence enclosure I made for them. several versions ago the update stated that that was fixed.