Outdated by Canon: As noted in the very last chapter, the creators knew that The Rebellion Story, being already in the works, would outdate this. However, there were other things that they could not anticipate:
The forms that the Demons took, based on the Nine Circles of Hell, was inspired from what their kind was called in Japanese (translated from "Majuu"). The original anime had yet to be dubbed when this story begin, at which point they would be called Wraithes, a specific type of demon. And even in Japan, it still took a while longer after the fic was completed before Wraith Arc would get published to detail how they'd actually operate canonically.
With Kazumi Magica still ongoing at the time, Kazumi herself was declared dead in order not to conflict with any plans still in place for that. As it turned out, she was actually a clone of someone named Michiru Kazusa, created using a Witch's heart along with Michiru's body, dictating that she would still assume the name Michiru in the story's past timeline. (Technically, though, that would also mean that Airi should not wield the same powers she had in canon, if she'd even become a Puella Magi at all, due to events that already had taken place in that series.)
, a side-story set during the early days of the war between the Puellae Magi and Vittoria. The second side-story, Pioneer