In light of the events of Wraith Arc, it's likely that what happened isn't that a new and worse form of corruption manifested ex nihilo but that the wraith born of Madoka and Homura's mutual love, who is integrated into Homura post-Wraith Arc, became a pseudo-witch.
The manga demonstrates that prolonged contact with old universe magic can cause wraiths to evolve into witch-like entities, including a copy of Walpurgisnacht itself. Specifically, the inciting magic was Homura's discarded shield of time manipulation -- which, in Homulilly's labyrinth, Homura had been using in place of the bow of memory manipulation. So, instead of becoming a regular witch that Madoka could freeze in the soul vault, the wraith part of her became a pseudo-witch. But since Madoka was already in the process of soul-conducting, Homura was able to interact with her, and by utilizing her anomalous power she could divide Madoka's divine powers apart from her physical body. Thus, Madoka gets to live a human life alongside her loved ones, the Law of Cycles gets to prevent witches, and everybody wins. Except Homura, who continues to be sad, and Kyubey, who gets mercilessly dunked on.