Did you get your pup from a pet store? Sometimes when they come from pet stores they are used to going in their cages and lose that instinct of not going where they sleep. Nikko has done the same thing in his crate and he is only in there over night. Maybe you are leaving him too long in there. I wish I had advice but all I can say is don't feel bad, there are other dogs out there that have done the same thing. Mine included