Puppy will make mistakes.  If he is nervous or afraid, this can lead to his using the bathroom in the house where he is not supposed to go.   

Yelling at puppy will only make the situation worse.  Rubbing his nose in his mess, besides being gross, is no way to discipline a puppy.   

Puppy pee pads that are treated with a scent which encourages them to go can be very helpful, especially if you have to leave them alone for a couple of hours and are afraid of accidents. 

Beware of puppy diarrhea, which can stunt its growth if not treated in a timely manner.