Just keep doing what you're doing, he's still a very young puppy still and will have a few accidents. However, I wouldn't freak out over him missing the litter box 1 time. As he goes through teething, neutering & the teen-times you may see him have accidents then too.
One other thing to consider, when mine get a little constipated, they kind of creep around as they try to poop. It could be that he started out in the litter box, but ended up outside when he actually pottied |