It happens very rarely but I encountered some issues with Entities Duplicating. I Have an auto carrot/wheat/potato farm with villagers and once i saw 2 villagers in each floor and there was supposed to be 1 villager in every floor farming(see picture). I also noticed that i had 2 hopper minecarts somewhere and there is supposed to only be only one. I have to mention that my computer is pretty bad and i lag a lot in my survival world which i think that's why entities duplicate!