Our little 3-year old boy likes to "vary" his routine from time to time as well. He has been trained for about 6-months now, but ocassionally he will just take a pee where he stands. I ignore it if I think it's a mistake but sometimes I feel he does it looking for attention and then I calmly tell him that Daddy will get cross if he doesn't try to go out to the loo (but I never actually get cross)
I walked into our sitting room the other day and he was as naked as the day he was born and was taking a leak in on top of one of Mammy's potted plants. When he saw the shock on my face he looked as if he was going to start crying, but then he gathered himself together and explained that he "was just giving the flowers a sup of wee wee ... they like wee wee" !!!
Children are crazy ... don't worry about your little boy, let him know it's wrong, but if I were you I'd try to figure it out between yourselves over a few weeks before you go down the GP route.