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 fan artists depicted Charlotte's human form as a humanized version of her first form. The secret to Nagisa's design is that it practically is that, just more subtle about it (white hair instead of pink, for example).
The film also canonizes some of the ideas about Kyoko and Sayaka's relationship (though it doesn't quite go all the way). Among others, it reveals that Sayaka did regret leaving Kyoko 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, due to becoming a part of the Law of Cycles and regaining memories of the previous timeline(s).
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.
The Other Darrin: In the European Spanish dub, Kyubey, Kyouko and Mami, who where originally voiced by Inmaculada Villalonga, Marga López and Violeta Bibiloni, respectively, were recast for the film. Mostly because the previous actresses were newcomers when they did the TV show (although Bibiloni was overall well received by fans), and their voice acting careers didn't take off afterwards. Plus, their lack of experience was obvious when compared to the rest of the cast. For the film, they casted three much more experienced voice actresses: Marta Barbarà for Kyubey, Graciela Molina for Kyouko (these two veterans are really big names in the Spaniard voice acting industry) and Eva Bau for Mami.
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, he wasn't satisfied with the ending he came up with. Producer Atsuhiro Iwakami and director Akiyuki Shinbo suggested Urobuchi 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!)
The guidebook for the movie, "Only You", shows that Nagisa's design used to resemble a Moe Anthropomorphism of Charlotte even moreso than her final design, complete with the short pink hair and more Charlotte-like twintails.