No, she's not clean from the poop. Bf poop does stain but usually stains clothes, there's poop still on her. You can use a soft baby wash cloth with water and a dap of unscented soap. I would put some diaper rash cream or brown some flour for the rash. Once it clears you can use an ointment like a&d, aquaphor, Vaseline to create a barrier.
No it's definitely not normal to still see a stain in my experience.. you can always try to dab it with cotton wool rather than using wipes as that may be kinder on the skin :) x