Didn't mean to imply that you didn't clean, but (after a bitch whelps) the area she's in, the pups, and even her own coat get covered by slime/discharge ... which (even though you can't see it) still can "rot" and get nasty, creating bacterial colonies which can cause infection/skin disorders.

This is why, after whelping, it is a good idea to bathe the pups and the bitch, then disinfect the area, and finally put them back in a clean environment.

Also keep in mind that (even after doing all of this) that pups shit and piss constantly, all-day and all-night, and so even if you disinfected the area + washed the pups after the birth, that the mama and pups will soon be covered with shit/piss/bacteria all over again. So it pays to wash the group and area at least once a week after that.

Betadine and Nolvasan shampoos are great for this IMO.

Good luck,

Jack