Adaptation Displacement: The anime is more popular by a bit because it's more easily accessible than the manga.
Alternative Character Interpretation: Takatsuki in the final few chapters. Was Takatsuki deciding she is fine with being a girl something that was foreshadowed and made sense character-wise? Or is Takatsuki in denial/confused about being trans due to a lack of support system (with Takatsuki barely talking with Nitori, Mako, and Yuki within the past few years) and people pressuring her to be cis (with her best friend Saori being unsupportive about Takatsuki transitioning and her job as a fashion model making her increasingly feminine presenting)?
Badass Decay: You'll often hear complaints how in elementary Takatsuki was a confident badass who beat up boys and stood up for his friends but by the end of the story he's far less secure in himself. In-series it makes sense, but that doesn't make fans less sour.
Base-Breaking Character: Saori is either an interesting and troubled Aloof Dark-Haired Girl who deconstructs several tropes or she's transphobe for repeatedly trying to get Takatsuki to detransition and a toxic friend.
Broken Base: The ending of the manga sharply divided fans due to how Takatsuki is treated after middle school. Many fans were fine with how her identifying as a girl (as detransitioning isn't unheard of) in the end, but many others, especially real-life trans boys, who previously found Takatsuki relatable, and were not very happy about this and felt it ruined the manga for them.
Takatsuki ends up with an Ambiguous Gender Identity and presenting as female, but most fans don't see her as cisgender. It's usually thought that she's either non-binary or a trans man but is going through a confusing period due to lack of support.
Takatsuki/Nitori is the most popular pairing in the manga, especially prior to Anna and Nitori dating, due to them being the resident trans boy and trans girl of the series. The fact that Takatsuki identifies as female in the end and Nitori ending up with Anna did little to sink the ship in many of the fans' eyes. The anime only helps with it cutting out the high school arc, focusing only on the middle school arc where Takatsuki and Nitori have a lot more moments together, adding some Ship Tease, and leaving the ending open for the fans to ship anything they want.
Takatsuki/Chiba is quite popular and works as a Ship Mate to Nitori/Anna.
Due to that Death of the Author issue above, an inverted version occurs when many fans refuse to read the manga, only watching the anime where the ending is open.
Faux Symbolism: Almost all colored artworks show the boy uniforms as being pastel colors when they're traditionally black. The anime, and the shading used in the manga, imply that they are black. It could be symbolically referring to their personalities, but it seems like it's just for artistic value (the artworks often are watercolored too, so it's a theme). Though considering how Shimura is with shading, they really could be pastel.
LGBT Fanbase: If you're in the trans sphere, some of the series (and the main/character pages attempts to describe what's going on with the gender stuff) will make you cringe in sympathy.
Mainstream Obscurity: It's known as one of the best depictions of transgender people in fiction, especially manga, but few people have read past elementary, or even more than a dozen chapters.
Memetic Molester: Yuki comes off as creepy to some fans. She doesn't mean anything malicious but a lot of her early scenes with Takatsuki in particular come off as flirty (even to Takatsuki). She also lets 9-12 year olds hang around her house and lets Takatsuki sleep in the same bed as her.
A part of the fanbase believes it's a Shoujo romance manga. It's actually Seinen and not a romance.
Especially prior to the mid-2010s, it wasn't uncommon to see people who think the protagonists are crossdressers instead of trans. Nitori was frequently thought of as a gay male, despite the fact she's predominantly interested in girls.
Chiba. After several volumes of being The Scrappy due to her temper and attitude, she was rescued near the end of middle school when she began cooling her head and rekindling her friendships.
Fumiya was redeemed after years of Saori's harsh remarks pointed at him seemingly got through to him, and the guy finally realized that he could be viewed as annoying.
Fumiya annoys fans with his mean attitude and the fact he keeps chasing Saori for years on end, despite her rejections. Dating Saori in high school didn't help his reception.
Momoko is bratty and unsympathetic. She's also a Satellite Character to Chizuru.
In high school Saori begins dating Fumiya with no pretense of liking him and the whole deal comes off as very "Why not?" Saori was never shown to be a terribly good girlfriend and they got no screentime romance which made fans think she didn't love him. Nope, they never break up or shown any signs of wanting to.
Takatsuki's storyline could've delved into the topic of trans-people who personally don't want to transition, don't identify exactly as one gender, or have doubts about their gender. But nope, she was a cis girl all along. Some feel the story might've benefited from more trans boy characters in general. YMMV of course, as Takatsuki's Ambiguous Gender Identity and bittersweet reactions to her feminine presentation and Nitori means that she could still identify as trans and is choosing not to come out, or that she is confused about her gender and is unable to voice her feelings to anyone. It's still a wasted plot and Downer Ending at best though.
Mako begins going out as a girl on her own and comes out to her mom but nothing ever comes of it. Likewise, she thought Yuki was a boy in middle school but we never get to see her reaction to her being a trans woman.
Anna is Nitori's girlfriend. Anna is a model. You think someone would leak she has a girlfriend and it would cause a stir but Anna hides their relationship quite well.
As elementary schoolers, the characters are given a lot of freedom which is not uncommon in Japan but is in some other countries.
Some points that western readers complain about are due to this. For example, the characters never see therapists for their gender issues, which fits the common Japanese views on avoiding therapy (which was especially prevalent during the period the manga was set).
Shiina's Crotch-Grab Sex Check of Takatsuki is assault on a child, though Shiina didn't know mean it in a sexual way. Aside from making Takatsuki want to cry, it's never brought up again and brushed off. Shina is otherwise a Cool Big Bro.
The manga began in the early 2000s and ended in the 2010s. It ran more-or-less in real time and shows the changing views on trans kids in Japan. Takatsuki and Nitori aren't pariahs but their parents and teachers don't know what to do about their gender issues. If the manga had begun in the mid-to-late 2010s, this might have been different, as more teens and preteens in Japan are coming out as trans and presenting as their gender at school.
What Do You Mean, It's Not for Kids?: The series is actually Seinen, as it ran in the seinen magazine Comic Beam. However, it's often been referred to as being aimed at kids due to most of the main characters being in elementary school at the start of the story, and is occasionally even mistaken for Shoujo. In America it's actually marketed at young adults and teenagers, which probably adds to the confusion.
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