Why Things Go Wrong
If the natural instinct to eliminate away from the sleeping area is missing, it usually means that the puppy was mishandled and not given the opportunity to eliminate outside of the sleeping area. In some cases, the puppy was not raised by a superclean mom that kept the whelping box free of stool.
In other cases, the puppy may have spent too much time in a cage in a pet store or a shelter and learned to go in her crate because there was no other option. A puppy that doesn't have this instinct can be a lot more difficult to housebreak.
This doesn't mean he can't learn to go in the appropriate place, but it will mean the whole process will take a little longer than average and require you to be more vigilant and flexible with your walking schedule.
Another problem with housebreaking occurs when humans confuse setting limits with being mean or allowing too much freedom too soon. When pups have free run of the house, they go to the bathroom whenever they have to go; as a result, they never learn to hold it. Other pups are not supervised well enough when they have freedom and sneak off to “go” somewhere inappropriate when no one is looking.
Almost all housebreaking problems are caused by human error, which is good news. It means that all you need to do is educate yourself so that you, too, can have a pooch that knows where to eliminate.