Passive mobs will despawn randomly in Survival. I have only observed it in Villagers and Cows but I think it affects other passive mobs too. It may only occur in Survival but I'm not sure. To replicate: Spawn Villager or Cow, then change to survival. Remember where they are or keep them locked in a container or something similar. Then go off quite far away, maybe 100-200 blocks for about 10-20 mins and you will find some or all the mobs have despawned.