It must be a daytime predator so I suspect a neighbor dog or one of the many field cats on patrol but could also be racoon, skunk, javelina, coyote, etc. I have to check the fence today to see if any evidence (feathers, blood, etc.). That run fence is a hodgepodge of 10 kinds of fencing mostly by previous owner so I'm sure I missed a gap somewhere in need of repair.If it was a predator, it might come back. I hope you will be able to find out and get to the bottom of the problem.
This kind of makes me want to be an expert at fencing & animal enclosures. I know it drives my DH crazy (as a professional building trades guy) to see the hodgepodge fencing and carpentry of our farm buildings. I've already decided the pallet pig pen has to go and a new pen built if we ever get pigs.