Your vet could be correct. He could also be wrong. There is no way of telling but as I said before, it doesn't sound like Duke's poops are a result of the diet because I think there would've been warning signs since he's been eating NVI for 6 days.
If your vet didn't perform a fecal to check for parasites or anything, then he doesn't really know but some foods can be rough on the puppy's digestive tract.
I would feed him bland diet until you get a normal stood. Once you get a normal stood, feed half bland and half NVI. If you see more diarrhea, I would go to the vet and revisit the idea of a fecal exam and another diet change.