this issue is not related to MCPE-12516. it is a baby chicken only bug. if it were related to MCPE-12516, then it would be resolved. it is still in 0.15.6.
set out a dispenser with a lever. set a cauldron next to it's output and cover it with something like a carpet. put a spawn egg in. if the egg spawns an adult, it will stay in the cauldron. if it spawns a baby, the baby will jump out. if you were to put lava over the cauldron so that when the baby grew it would be cooked, it doesnt work because the baby always jumps out and dies.
i can get adult chickens to stay in a cauldron if I place a carpet on top, but baby chickens will leave, even if the cauldron is surrounded by stone blocks. i used a dispenser and spawn eggs to get the adult chickens in fine, and used regular eggs in the dispenser to put the baby chickens in. i did it in creative on win10 Beta.
I do have animals and villagers that clip. now that my pens are below ground, they die instead of getting free. I will get a villager on the outside but it is normally a baby that clips when being bred. I think that there could be less clipping, but I believe that it happens mostly when the chunks are being loaded. its not like 100 of each chickens/cows/pigs suddenly all ran to the dirt walls then suffocated. my LAN world does crash, but I haven't attributed any activity to the crashes. I think it probably has to do with lag. I have never gotten any extra XP, but when other people connect to my win10BE world and enter my zombie/skeleton farms, they can kill one skeleton and get anywhere between normal xp and, so far 40 LEVELS of xp from a single kill. if the game cant keep up with all the tracking, maybe that's why it looses track of items and mobs disappear.
Windows 10 Beta - I have had to reseed my village several times. I have a large house with no doors that held my 30 villagers. I had empty houses with doors. All 30 villagers slowly disappeared. i switched to createive, put in 12 villagers, and they bred up to 30 again, then slowly dwindled to zero. had pig, chicken and cow farms. one day i looked they were full, the next they were completely empty. This is my biggest outstanding issue as well. The villagers aren't a big deal since there isnt trading yet, but the animals are a huge pain.
I can confirm this happens on my windows 10 pc. first everytime I entered the nether i would get the same spider. then it was a persistent zombie pigman that would track me down every time i logged in. finally i actually logged off every time in front of the portal so I would just get it over with. then I read Jacob's post, So I threw in a diamond. now every time I log off and on and enter the portal i get a one-hit zombie and a Diamond. i can finally move up from enchanted gold drops to diamond armor! - seriously, it should be fixed.
i have a 0.12 world that now spawns more ghasts in 0.13 than it did in 0.12. this is MP survival.
I have one player in multiplayer that looses items in the furnace, the host never does. one other player has problems starting the furnace, but hasnt lost anything. will make sure that nobody shift clicks, to see if that is the only case.
Well, with animals res pawing on their own in the wild, and villagers can be built, one doesn't have to go into cheat mode to fix the issue. We all live with this. I don't leave saddles and armor on my horses anymore, I keep a chest at my corral.
Granted, I wish this didn't happen. I hate keeping my villagers locked in a small room to keep them breeding.
Here's to hoping they resolve this soon.