I just discovered this, too!! I found two of my chickens this morning meandering around the run even though the coop was locked up for the night...further investigation led me to discover a tunnel they had dug under the sand box beneath their roosts, the entry to which was obscured by their plastic feed tubs!!!! The tunnel stretched a few feet under and out into the coop behind the bench and treat area.
Seriously, chickens?!?! They've even started to dig a hole under the front door of the run to the outside world.

It turns out that chickens' worst predators might be themselves.