When you have a potential prey animal outside even in a building or run you should expect it to happen at least once. I've lost guinea pigs, rabbits, chickens.... Many in secure pens and some free ranging the backyard. Expect it. Be prepared for it. No matter what you do it will happen at least once.
You can get netting in the garden section for throwing over berry bushes and similar to keep wild animals out of them. It's only a few bucks for a huge piece but I generally just keep my chicks inside in a large rabbit/guinea pig cage (homemade 3x6') for about 6weeks and then in the 170sq ft coop until they are near full grown. They can leave the coop if they really want but the doorway is a foot up and then has a several inch bar a couple inches above that so the smaller ones would have to fly to get over it. The bantams generally don't try it until they are 4-5months old. If I put them out in the coop sooner than 6weeks I'd probably build a temporary pen in there to keep them locked up while still letting my adults out to free range. If you have no adults to let out then just keep the chicks in until they are big enough to not be carried off by anything and everything that comes by.