Fans were quick to latch onto Poorfag-chan, a nameless and dialogueless classmate of Madoka whose only distinguishing feature is that she can be seen taking notes with a pen and paper while the rest of the class uses laptops. The Internet quickly decided that she was an orphan who lives in a cardboard box and has to scavenge though dumpsters to find school supplies; despite this, she is always cheerful and never gives in to despair ( which explains why Kyubey hasn't approached her about becoming a magical girl). She also writes letters to her dead mother that always begin "Dear Mother in Heaven." A couple of fans have decided that she makes an appearance near the end of the Rebellion movie, walking to school with a boy. Given that everything has turned into a Lotus-Eater Machine at that point...
As a lesser example, there's also Clip-girl, another nameless background classmate who is seen looking at Homura while sitting at her desk. Fans have proceeded to take this as evidence of a romantic crush.
End of series spoilers: The entire concept of a magical girl Valhalla, is likely but unconfirmed. Word of God refers to Madoka taking magical girls to a "different universe" which could mean anything. There's also the manga ending, but that's just a scene of Madoka and Homura in white, which could also be anything. Oh, and the monsters that appear at the end of the series are called majuu in the original Japanese, which means "magical beast". "Demon" was a Woolseyism made-up by fansubs. The English dub uses "Wraith".
The words mahou shojou being translated as "Puella Magi" - even the American version is going with "magical girl". In fact, the words "Puella Magi" are never spoken in the series. They only appear once at the very end... as part of the series's title written in Cypher Language.
The funny thing is that Puella Magi does get used as translation for mahou shojou in some dubs, like the Spanish one (which got some controversy due to it).
"Puella Magi" actually pops up in Rebellion, but as part of the name of a magical girl team. The team's full name is "Puella Magi Holy Quintet", which is possibly a reference to Magica Quartet, the team name of the series's creators.
The Stinger. Oh boy, The Stinger. Here's what Word of God has said about it: It wasn't intended to be a Sequel Hook, it's supposedly set outside Japan, and it's an Homage to Blade. Anything else - such as being set in the far future, Homura dying afterwards or even Homura transforming into something else is pure speculation.
Homura's family situation, or lack thereof. There is no indication in the series that Homura has any sort of family - even her residence only has her name on the nameplate (much like Mami's apartment). In episode 10 she's implied to be filling out school transfer forms while still in the hospital, all by herself. The vast majority of fans have decided that she's Conveniently an Orphan. On the other hand, in the first Drama CD she offhandedly mentions that her family won't mind if she stays out late...0
Anything about the witches'Backstories. Anything. The one universally accepted by the fandom is Charlotte being a cancer patient who wished to cure her illness so she could eat the food she liked though it's important to note that the Official Guidebook has a line implying that her mother was in fact the sick one, and Charlotte's regret — making a wish to share with her mother's favorite food with her, instead of curing her disease — is the what caused her to become a witch. On the other hand, that entry was for a prototype witch, and not Charlotte herself.
Kyoko's wish-derived powers. Fans pegged it as some kind of Mind Control (based on her wish causing everyone to listen to her father) until Word of God said that it was never seen in the series and revolved around light and illusions. The third Drama CD revealed it was actually a Doppleganger Attack.
There were also some assumptions about her family, particularly her sister's name. The third Drama CD gave it as Momo.
For the longest time, fans thought Mami's wish was "I don't want to die alone" mostly for the sake of irony. Word of God later said it was "to connect to life" (i.e. "I want to stay alive"). This then became God Never Said That when some people (on this wiki, even) read it as "to connect to lives", which has a different meaning altogether.
Kyouko is sometimes portrayed as wearing a Mitakihara middle school girl's uniform in fanart, like the other four magical girls do. However, not only is Kyouko from another city, but it's indicated that she doesn't even attend school.
There is a reason for this: The On the Next segement of each Madoka Magica episode included an image drawn by a guest artist. The one for the last episode was drawn by Madoka Magica's character designer Ume Aoki and contained an image of all the magical girls in the same school uniform. In short, while it's not exactly canon, it is based on official art. And then the trailer for the third movie shows Kyoko in the school uniform, making it canon.
Homura's timeline count. In the series, it's shown to be five at the least. Though it's a point of debate among the more technically-minded fans, most fanfic writers take a more dramatic approach, suggesting anywhere from several dozen to several hundred, with some heading into the thousands. Stories that don't provide a count still often show her acting as if resetting the timeline is almost meaningless to her. No matter which way, they all seem to agree that the ones seen in the series were only a very small fraction of what she went through. Word of God confirmed this to a degree, claiming that it was "approaching 100."
The final fates ofOriko, Kirika, and Yuma in other timelines. Though Yuma's fate seems variable, just about everyone who thinks Oriko and Kirika exist in other timelines suggests that Homura assassinates them early on.
Are magical girls immortal? The series is pretty ambiguous on the issue; Mami and Kyoko both age, but Homura doesn't (though her powers could be a factor). A great number of fans, though, have suggested that magical girls have some form of eternal youth, either being able to freeze their age or being ageless as a consequence of having a body that's already dead.
A fairly minor one, but many fanartists draw Homura with surgical scar along her chest as a sign of her alluded heart problem. Though there are (with varied level of canonicity) arts from the animation staffs of the minimally dressed Homura and none of them sporting that scar, many like that one detail for giving a sign of realism to her Ill Girl past.
They're all lesbian. No exception. The fanon especially leans towards Homura (for crossing the "Ambigious Relationship" line with Madoka too many times to count) and Kyoko (the tough tomboy who changed her whole attitude and eventually gave up her life for Sayaka.
Hitomi being a magical girl in past timeline(s) is pretty much accepted by all of the fandom.