Do you have a photo of the holes? I had a rat issue last year. Only real fix are the heavy duty traps baited with peanut butter. You have to be diligent about picking them up in the AM and replace them in the PM so you don't catch other wildlife. I also put a camera inside the coop and saw a chipmunk and a few mice squeezing in one area which we were able to seal up. Traps caught a few rats and I don't want to jinx anything but we didn't see any any evidence after that.