Yeah that was a concern for me, especially since my coop is elevated slightly to keep it off the moisture-laden soil, but definitely not enough for me to access the underside in case birds got down under there.Personally having seen what chickens do with dirt, I don't want my birds under the coop building under-mining the foundation. Literally. So my coop is not in my run.
My solution was to skirt the coop with hardware cloth, as you can see at the bottom perimeter Which of course is an extra expense. Instead of aproning outward as with the run, the excess is tucked under the coop.
Also I should probably mention, my flock took to peeling paint off the coop as well, yet another annoyance!
I snugly wrapped the bottom couple of feet with stiff bird netting secured with roofing screws and that put a stop to it, but weird things like that are just another "extra" to account for.

