They did....Apparently you didn't bury your hardware cloth when you built your run. It's really the first step in preventing predators and pests.
You can still lay 12" concrete pavers around the exterior perimeter to discourage digging. Make sure they're tight to your structure/hardware cloth and tight to one another.
...tho 6" is nothing to a rat.6" of hardwire is buried around the run,
They'll go right under pavers too.
@The Moonshiner's got it right.