do you, or a close neighbor have chickens, or other fowl? because this could be rats. but if they are coming into your shed, there should be rat droppings inside.. what you could try, is get a pack of 4 insect fogger cans, and set them off inside the shed, let that sit for the recommended time, what ever this is will either be killed, or will flee, I'd look outside for anything fleeing that spray.. you could put down sheet metal over the floor, it's pretty cheap, and nothing will be getting in anymore, but if it's something that eats wood, you could have big structural problems.. you could also try getting a funnel, and pouring rat killer down each hole..