House soiling is a spatial problem. Your puppy dog has been allowed to eliminate in the wrong place. House soiling quickly becomes a bad habit because dogs develop strong location, substrate, and olfactory preferences for their improvised indoor toilet areas. To house-train your puppy dog: first, prevent any more mistakes; and second, teach your puppy dog where you would like him to eliminate.
Crate Training - errorless learning
Ian Dunbar, January 2011 Dog Star Daily