when you reload a single player world if you have an excess of animals in a pin or just a single block area and they push each other into a wall on reload it will kill them even if they are encased in mostly glass they will still die off to very low numbers compared to what I would expect there to be in the farm. The most recent example would be chickens encased in wood and when I opened the world I heard chickens dying and I found drops from at least 6 chickens. The first example that I came across was 24 cows in a 4x4x2 dirt pin that I was about to put in my farm and I would find drops from them dying when I would sleep. the same group of cows (groups of 24 in 4 1x1 pins) randomly reduced in numbers to 5-7.

I believe this bug is due to the addition of animals being able to collide with players in 1.9 (which I barely played) causing the game to derp out when the world loads. or you are loading in entities before the terrain and that is allowing mobs to explode in all directions then it loads in the blocks and animals die of suffocation