I was wondering, do you by chance line the crate with newspaper? Some breeders start potty training with newspaper and maybe he's going on the newspaper instead? and if since he's so young and just couldn't hold it until you get home and has done his buisness in the crate once or twice already he may have just marked it as one of his potty spots and even after cleaning the area it's hard to break the cycle of going there even if it's wrong. That's from my experience anyway. I decided not to use wee wee pads and go for the newspaper with Kiko because I knew he understood that already as a potty spot and so far it has worked well for me. Maybe if the breeder was using newspaper you could give that a little test? I dunno just a suggestion..I had the same problem with pads with my first a long time ago, the newspaper has worked much better this time around. Good luck with whatever you choose
