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I'd put money on them bein' collapsed muskrat dens.

Now that makes sense. It also sucks, but might explain why the dog went nuts and the ease it had cutting thru the soil. The area where these are is a 3:1 or 4:1 slope down to about 9 feet deep, so it will be difficult to see entry ruts under the waterline. Next trip, I'll examine more closely.
I can't say that I have ever seen a MR, but I'm not there enough to be anywhere near certain one way or t'other.