[meleechampion]

Why do you think this happens?

I have four realms connected, with no more than 80 sheep in each one. They're penned in, cannot cross to the other realms thus breaking the 100 mob limit. They're walled off, so people aren't killing them.

Any tips to help keep them safe?

(can't figure out if the attachments worked, images here: http://imgur.com/a/yFWUk)

[Prodigy9]

Could there be other mobs that spawn in the area? You'd notice if there were things spawning in the middle of the sheep pens... but could there be monsters spawning in a cave system or along the subway?

[meleechampion]

could be, I'll have to be more careful about lighting and hope that it helps

[monkeychunks]

Maby a mob spawner under it? Someone could,also enderpearl in.

[WMBOClan]

My cow were doing that. The groud was only one block thick and they were falling through and gettinh through the wall which too were ony one block thick. Double up.

[Soul K]

Unless stone fencing doesnt work like wood fencing that could the the problem but you do have wood posts with a torch on it and that should be enough since its sorta like how I have my cow farmer set up.
Other then that I dont know.