Clean the carpet. He's marking over the pee and poop smells on the floor. Cheap solution to it is white vinegar and water, half and half, soak it right into the padding. Smells a little, but gets rid of the enzymes that make it smell to the pup.
You can also crate her at night when you are sleeping so she cannot have the chance to do this, or gate off the particular room you do this in, or stop changing the baby on the floor (or even get a mat to lay on the floor to lay the baby on).
ADD: No, it won't just torment her. Actually, because you're pregnant and home a lot, this is the PERFECT time to crate train her. You can start out slow and be much more consistant than someone who leaves for work during the day. Our dogs had a bumpy start becaus I have work and HAD to put them in there or they'd tear the house up, so our work was slow, but they adjust as well. "Go home" means 'go to your crate' with them. They still have their moments we're working out, but for the most part they're utterly silent and totally chill with it.