I don't know the meal routine or even what is recommended here by our fellow PT'rs, but I have never fed my puppies 3 meals. I have always fed them 2. Once in the AM - when they/I get up and a second around 5:00 PM. I have rarely if ever had a pooping problem inside - it is usually the peeing that is the crux of housebreaking.
I think it is becuase he is eating twice (PM and Night) before he goes to sleep that he is waking up and "Hey... when you gotta go - ya gotta go"!!!
Try altering you schedule for sure and see if you can't get him going poop (first thing in the AM).
Also - are you crate training, because if you are it is highly unusual for a dog/pup to poop in their own space - crate/den. HE MUST "REALLY" HAVE TO GO!
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