Base Breaker: While not as much today, back when this series was first aired, it got quite a bit of backlash at first, due to the lowered hand-to-hand combat elements compared to the previous seasons and feeling like too much of a retraux of the original. Nowadays, the series is seen with much more respect and is overall much more enjoyed, and it's given its due for introducing the now standard Dark Magical Girl joining the heroines' side. The darker plot and the flight mechanics to mix the elements it introduced with some new hand-to-hand fights near the series end may have something to do with it as well. The series still has some detractors, though not as much or as volatile about it as it used to.
Les Yay: Saki and Mai (principally in the movie), and later these two with Kaoru and Michiru, combined with Incest Subtext.
The first ED had lots of holding-hands shots between Saki and Mai.
Memetic Molester: Or more precisely, Memetic Lolicon; in-series Saki's little sister Minori is the Morality Pet of Kaoru, whose protectiveness and affection then degraded into perverted jokes quickly in fanworks.
Out-of-Character Moment: Many think that the Non-Serial Movie is this, mostly from Saki. As the relationship between Saki and Mai is extremely stable and understanding since the beginning, a Feud Episode is just out of character of them note There's an episode already where they have a misunderstanding, but they don't fight like in the movie. Instead, they go for a Twice Shy scenario. Not to mention Saki's dense Jerk Ass behavior doesn't endear anyone. Almost all of the fans will recommend avoiding the movie for this very reason.