The first couple of years we had our pond, we got a nice collection of collapsed burrows I have always blamed on turtles. The typical one would be a semicircle about 5 inches across and 3 inches deep, connecting to the water at each end. There was one bigger one that meandered up the side of the dam, just above the compacted core (that one I dug out in it's entirety and repacked with a spud bar). Entrances were all just below the waterline.
We've never seen any muskrats or other mammalian vermin that could have dug them, but we did have turtles then.
I stopped worrying about the turtles and realized I could back fill the collapsed holes with dirt from the pond bottom faster than the turtles could dig them. I have not seen any new collapsed burrows for a couple of years.