Okay, so I have seen many threads about people's farm animals disappearing. This might be the solution for those kinds of problems. Give me your feedback if it worked or not because I tried it on a small scaled farm and it worked.

http://www.youtube.com/watch?v=BWj0LaQcedg&list=UUChaPGDM0d6YQv2yyVoVfGg&index=1&feature=plcp

This does work, however mobs despawn if a player isn't a certain amount of blocks within it. Animals disappear mainly because of them despawning, and sometimes when the glitch into walls.

They despawn? I though in 1.8 they couldn't despawn anymore

Yes, they do despawn. I had once trapped 2 sheep. I went back on a day later to see that they are gone. I know for a fact they weren't killed as it was in my house, which is protected, and I could only go into it. There are also some threads on animals disappearing and some of them were due to them despawning.

Animals cannot despawn anymore (after the 1.8 update), but every time the plugins for the server are reloaded, they are "despawned", meaning that their data values are wiped from the map. This is not because a player is not within distance of the animal.

Sadly, there is no way of preventing this, other than getting a spawner for the specific animal (which can be quite costly).

Oh, no wonder why this happens. Thanks for the clarification, Anonymous.