How old are the babies?
Let's face it, things that come out of bodies don't smell like roses. Add more than one animal and the smell multiplies. Also based on checking a different thread you mentioned they were born mid July, all you should be doing is a quick spot clean away from the igloo. So any near igloo accidents would still be there.
They're three weeks old and I've been scooping up bedding and putting fresh bedding in, especially because the mom makes a mess with her food and water for some reason every night. I figured it was normal but I just wanted to double check
If you've got babies, you're going to have smell. No way around it. Since you can't do a full cage clean until they're weened, that's how it's going to be. Once they're weened and everyone is separated out into their own homes and you can properly clean again, the smell should reduce dramatically.