I am playing Vanilla Survival mode. I create farms and breed quite a few animals. I have different size pens to hold each. When I go a few hills away or underground to my mines for 15-20 minutes or more and return I always return to my farms always having only 2 animals. Recently i had 10 cows, 20+ sheep and about 8 chickens. No matter what I do it happens. This happened in previous versions of MCPE as well.