Seems like Madoka's wish for all Witches to regain their human bodies back is not perfect; look at how black and tainted Charlotte's Soul Gem is.

Maybe the author think, the original for charlotte's Soul gem colour is kind of black

That’s like running a car without knowing how much gas is left in the tank isn’t it ?

Yup - she didn't see the taint in her soul gem so she became a witch early. Makes sense.