I was trying to move a witch from my witch farm into the Nether for some decoration around the portal on the Nether side. What I expected was that the witch would enter the portal and when I arrived after, it would be ready to be moved into its cell. However what did happen was the witch has completely disappeared.

I thought this might be a server glitch, but the same thing happened in my single player world, in both survival and creative, with both naturally spawned witches and those from a spawn egg.

I did some further testing, and found that if I left a few spare witches in the Overworld, upon returning they would all be gone. I never noticed this in 1.8.

Also I did the same thing in a brand new world and I could not get a witch to move from the Overworld into the Nether. BUT I did find some inconsistencies. In the end I did manage to get 2 witches through, but it involved pushing her, and then instantly getting into the portal behind her, and even then that only worked 2/6 attempts.

Not sure if this affects other mobs, as I only tested with witches. I did spawn about 40 on the portal frame itself and then followed them through, and managed to see them arrive in the Nether, but it was an instant despawn for all of them.

Steps to recreate:
1) Load a new world.
2) Create a portal to the Nether and go through it.
3) Go back to the Overworld and enter survival mode.
4) Spawn a witch or 2, and get them to enter the portal.
5) Follow them and watch as they disappear.