You are probably giving the puppy too much free run of the house. I would get a pen and keep the puppy in it unless you are right there with him. At this age you have to keep track of him at all times. It will pay off in the long run before just going everywhere gets to be a habit. At 12 weeks they have to go often and when they are just running loose in a big area, they just go where they are as they do not have the control to run back to where the pee pads are. If you do not have a pen, you can block off his access to the rest of the house with gates.