I'm thinking it may be a small mouse or something, looking for bugs, or possible a large beetle, but there is not "evidence" left behind by the culprit.
I know it is not soil washing out because this has happened on days I did not water the plants, and that it didn't rain on.
Here is a picture that shows that they are not going for the rhizomes because there is a rhizome that has been dug up but has no damage.

Sorry that you can't really tell there's a hole there, but there is, and it's about 2" deep.
I cant say for sure that they aren't harming the root, because today when i checked there were a few roots showing, but little damage if any was done.
If anyone can help ID the pest causing these hole it would be great.
If not, it just might have to end in a long night, tons of caffeine, and my good ole' BB gun

...or maybe I'll just use some mouse traps
