Is he neutered? I agree with the opinions about it being territorial, even if he's not aggressive with the puppy he can still want to assert his dominance, and right now he's feeling the need to 'mark his boundaries' and re-establish his turf. Some un-neutered dogs will do this too, but it's more of a problem with intact males.
The behavior may stop on its own once he's more comfortable in his position as The Dog, lol but to be proactive you could start over with the housetraining basics, take him out very frequenltly and pile on the praise and treats when he uses the bathroom in an appropriate place.