OntarioSheltie
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and what melissa advised is actually what we had to do in the beginning when he would wait 45 minutes to pee when outside and he caught on within a couple days, so maybe we will need to do this when he tries to poop inside.
With pups its some times necessary to go back to square one. We had to at some point with both of our pups.
I know can be frustrating initially, waiting 45+ minutes for them to go, but I've found that once they figure it out it sticks with them.
Milo, my parents sheltie you could almost see the light bulb go on over his head. He literally never went in the house again, unless we missed his signal and didn't get him out fast enough.
With my rescue Toby, he managed to hold his pee for some insane number of hours before finally going in the correct spot (he wasn't a pup). But we never had a problem with him again either.
Try to hang in there, he'll get it eventually.

Oh, and that's great that you're teaching him to relieve himself on command. Our girls are trained to go on command, which is extremely helpful.