So earlier today i bought 100 sheep eggs... had a entcount on my second res of 0... come back five mins... instead of my 100 sheep being there.... there is 66 my sheep dissapeared!
I believe this is a problem with mojang not EMC There is nothing they can do about it but wait till the next update.
Sheep used to die if you dint sit next to them and watch them grow up, Ie: if you un egged a sheep then ported away when you come back they would die. Not sure if that still happens but that might be what happened :/
My favorite trick to keep my animals in place is line the outsides of the walls with water. Keeps them from suffocating in walls or walking through fences.