Is it possible that this issue is somehow related to when you enter the world, and it is "building" the terrain? I just went back and forth from the Nether to the Overland a few times, and noticed some of my animals had dissapeared.
This should NOT be considered resolved!
I can confirm this just happened to me yesterday (11/2/15) in MCPE version 0.12.3 on iOS
I have a barn with 4 no-escape pens holding pigs, cows, sheep and chickens. One minute I had several in each pen, the next I had NO chickens, ONE cow, a few sheep, and I couldn't tell if I lost any pigs or not.
Yes, very similar. Same issue really. This report was created first though. The two should be merged.