Draco in Leather Pants: A lot of fangirls tend to treat her male leads in works this way (sometimes even literally). Sakuya and Hakuon are good examples of these, due to their good looks and their genuinely crappy childhoods, but while the second point does explain why they are... the way that they are, that still does not excuse their jerkass tendencies, and their treatment of their love interests borders on Rape Is Love multiple times.
Those chins make the readers want to mistake them for weapons.
Harsher in Hindsight: Lots of people have wondered if, considering the very polemic plots of her stories, Mayu Shinjo was an abuse victim writing what she knows. It turns out that Shinjo actually was subjected to huge abuse coming from the Shogakukan editors, and the details are pretty nightmarish. And she's not the only Shogakukan author that was treated in such ways, as the lawsuit byMakoto Raiku says.
Also, in Haou Airen there's the scene in which the barely teenaged Fuuron and Hakuron meet and decide to work together, and you could cut the UST with a knife there.
Narm: Sometimes her stories are so wangsty and unbelievable that they come off as funny. Some summaries of Haou Airen have made people actually laugh their butts off at how ridiculous the story sounds.
Nightmare Fuel: The rape scenes. They're supposed to be romantic, but...
The entire scene in Haou Airen where Reilan deploys her Thanatos Gambit via setting up Kurumi to be gangraped and then deliberately getting Hakuron to kill her. Say what you will about the manga as a whole, but that scene was particularly well-done.
Uncanny Valley: Everybody looks off when you see them from the side.
Unfortunate Implications: These stories are very likely to offend most readers' sensibilities, and even those who consider themselves less "sensitive" will feel uncomfortable at some point.
In Ai Ore Love Me: It's okay for a boy to look like a girl, but if a girl looks like a boy, she's an abomination. The chapter involving lesbians is pretty cringe-inducing too.
Unintentionally Unsympathetic: In Ai Ore Love Me, we're supposed to "feel bad" for Akira, the male lead. He's a complete asshole and really creepy to boot. At least he gets humiliated more than once.
Wangst: Her works have melodrama written all over it, but it can be really overblown at times.
What Do You Mean It's for Kids?: A lesser known work of hers, Heart no Daiya, ran in Ribon magazine. Ribon is aimed at girls from 9 to 14 years old. Just to let you know, it had implied pedophilia.