Usually when something like that happens, it's because of something screwing with physics, or a bad redstone problem, or a spawned mob glitch. I'm guessing the third, especially since there's an acknowledged bug having to do with the overspawning of squids. I just went and checked it myself and it seemed ok, but we'll have to keep an eye on it... if worse comes to worse, we can try turning off monsters/animals, rebooting the server, logging in to make sure all the generated npcs are eliminated, then turning them back on and rebooting again.... but I think everybody logging out of the server for the time that they have might have accomplished the same thing.
I could be wrong, and it could be something nobody's even thought of yet.