It's common in fanart to include Charlotte with the other magical girls and Kyubey as though she was some kind of extra mascot. This actually happens in the movie.
And while we're on the subject most fanartists depicted Charlotte's human form as a Moe Anthropomorphism of herself. The secret to Nagisa's design is that it practically is a Moe Anthropomorphism of Charlotte, it's just more subtle about it.
The film also canonizes some of the ideas about Kyouko and Sayaka's relationship (though it doesn't quite go all the way). Among others, it reveals that Sayaka did regret leaving Kyouko behind. On the other hand, it's implied that Sayaka feels this way because she has become aware of how much Kyoko cared about her.
Homura becoming the devil to Madoka's god. It wasn't quite the way anyone expected, though...
Meaningful Release Date: Possibly unintentional, but the movie premiered in Japan a few days before Halloween. Homura says she's the pumpkin in the Cake Song. See also Fridge Brilliance in the Fridge page.
Reality Subtext: At the end of the movie Madoka says she's been living in America for about three years. Puella Magi Madoka Magica began in early January 2011, while Rebellion premiered in late October 2013—a little less than three years.
Originally Rebellion was plotted as the anime's second season. However, the creators couldn't find a way to make it long enough. Then some other staffers began wondering if they could make a movie adaptation of the anime...
When he began to come up with the plot, Gen Urobuchi originally planned on having a more conclusive ending. However, producer Atsuhiro Iwakami and director Akiyuki Shinbo suggested he make the ending more open-ended. In fact the movie's final twist was Shinbo's idea...which Urobuchi acknowledgesas the catalyst for his screenplay (that is, he didn't even have a screenplay until he got that idea). Warning: Major spoilers in the links!