I've had the same problem the last couple years. I think the chipmunks and moles dig tunnels and water can get under some plants and/or let cold air under plants to freeze roots. I am keeping any tromped down that Ive seen this summer. ((Tunnels, that is ))
It could also be that mice and/or voles used these tunnels to eat the roots (especially in winter). Moles are only carnivorous, so wouldn't be eating roots. I've never seen a vole in my yard, but have suspicions.
I am getting more aggressive this year trying to repel digging critters out of the beds.
I am wanting to fertilize mine this fall, but all research says Sept too late.