This is a tough one, and it dramatically impacts the ability to house train a dog. It is a natural instinct for a dog to desire to stay clean, so if it will go to the bathroom in the crate and lay in it consistently, then there is good chance your dog has suppressed his natural instinct to stay clean. Other possibilities are sometimes owners put too much bedding in the crate that soaks urine up, so the dog can actually urinate in the crate and not have to “lay” in it. Sometimes the crate is way too big, also allowing the dog to urinate on one side and hang out on the other. Sometimes anxiety about being in the crate, whether that is from containment phobia or bad association of the crate, can cause urine or bowel movements.