I'm trying to build a village from scratch. But mobs keep de-spawning. 

What I expected to happen was...:
I cured Zombie Villagers, and I keep them trapped on boats with boxes around them so Hostiles can't hurt them. The plan was to cure them as I see them, finish the village and release the villagers once the city wall is built. 

What actually happened was...:
A few days would pass in-game, I could be close or our mining, but occasionally I'd return to find the villager I had trapped was gone. 
Cows and Sheep have disappeared from their pens too. 

Steps to Reproduce:
I don't know if it's a random chance. But the situation I'm in is; ** 
1. The villagers were cured from zombies.
2. They were kept in boats.
3. They were maxed out on their trades.
4. The location of my village/base is naturally generated lake that I've paved over with stone.