If you were on the west coast I'd guess it was a grey digger ground squirrel. But they don't reach Massachusetts to my knowledge.
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So you said it might be a squirrel, and after doing some general googling I think it might be even thought it seems odd. I found this diagram from the Iowa state university website and based on you saying there was also a hole in the garden it points to a ground squirrel to me.
Even if it is a ground squirrel, how would she get it to stop tunneling and creating these weak spots in her design? Sounds like there may be a market for a coop version of a squirrel baffle! Naughty squirrels...
Even tho this is title 'Massachusetts', the range described is all out west.I found this website about Massachusetts ground squirrels, interesting read. http://www.800critter.com/massachusetts_groundsquirrels.html
not sure if you have a tree that drops nuts around your coop, but it could be possible if squirrels live in the same place their whole life that they remember nuts being in that spot and came back to dig them up?