Having Nagisa around gives Homura and Mami an excuse to throw down, which apparently they wanted to do from the beginning since Mami didn't get to show off her skills well in the series. Using "Bebe" as the mechanism probably was just fan service, though.
Moving on, episode 10 of the series shows Homura distancing herself from Madoka more and more as the loops wore on. Rebellion is the ultimate culmination of that: Homura's sought to save Madoka for what may well be a thousand loops. When she gets to meet Madoka again after she erases her own existence, our rather psychotic heroine finds one more way to "save" her, only realizing after it was too late that she'd done Madoka no favor and quite possibly severed any chance of them being close again.