This is typical. My dogs have done this quite often. Your dog is a rescue. He is simply making his mark, so to speak. I'd say after a few weeks and once he's settled the marking and lying it will not be a problem. As for the crate, has he been trained to be in one for a while or is this is first time? First time, he won't be used to it, second time, he'll learn not to Shi* where he sleeps.