I went to the nether, then accidentally threw my sword into the nether portal after which it disappeared. I looked around a little both in the Overworld and Nether, but couldn't find it. I went back and wandered around and then angered a pigman and proceeded to run to my portal and go back to the Overworld. When i came back, all the friendly animals in my area (mainly my dog who had a nametag and a bunch of cows I had penned up) where gone.

I don't exactly know what the glitch was related to, but i had gone into the nether before and this didn't happen, until i angered the pigmen.