Over the past few days, I have noticed about 10-15 of these shallow holes in my flower garden, filled with seeds and sprouts. I can’t tell if the seeds are sprouting or if the animal is placing the sprouts there. There are also deeper holes that look like traditional chipmunk or squirrel holes.
Always helps to know where you live when answering these types of questions. 
Ah, sorry. I live in New Hampshire.