I've just made a villager breeder so I'm in the process of making a captured zombie turn my villagers so I can cure them. My problem is that I've named 3 zombies, 2 of which i got to pick up sticks. I'll go mining and come back to him being gone, even though I have him in an underground room with no exits. Why is this happening and can I do something to fix it?
Are there iron golems or anything else around that could be killing him? Is his room set up in such a way that he's walking into a spot he's suffocating in? Is daylight somehow hitting him and setting him on fire? Perhaps a minecart is scooping him up and putting him in a spot where he suffocates?
The room is underground, no golems are spawning near him, he's in a glass enclosure, there is a rail going in and out, and the minecart is used for villager transport only. So there is no way he can get into the minecart.
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What version are you playing? There was a bug before 1.15, MC-27535, which would cause mobs to despawn, even with name tags. If the mob is still despawning, even in 1.16, it could be a recurring issue, or it's just your game.