It's a natural puppy instinct to NOT pee/poo outside their "cove". This is to prevent predators in finding them with their smells all round the area. Sometimes it takes longer for some to go outside.
A neighbor of mine got a puppy, and they too where having a hard time with pee/poo inside. I told them to just take it easy, and don't punish. Spend a good time outside, and award when he/she does go outside. It took until their dog was 8 months until he started going regularly outside.