I had an entire ranch set up with all the colors of the sheep. After the new Nether Update, I noticed that over half of my sheep were missing from an entirely closed in and lit up barn. (Roughly is roughly 16 colored (dyed) sheep)

I also have issues with my bees disappearing as well. I've tried everything from removing harmful plants to fencing in my farm/beehives. In one area there was a completely sealed green house; fully lit, with roughly 12 bees. I returned to the greenhouse about a "minecraft" day later and all bees except one; including nametagged bees were gone.

My Iron Golems are also randomly despawning.