These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Replacement Scrappy: After Gen dies, Sen and Souji as his replacements, the former is a sissy Dude Looks Like a Lady and the latter isn't as emotionally engaging (makes sense his emotions are even more low key than Gen's) and a great deal of the last part of the plot is focused on him rather than the more pressing matters of the Shadow Organization.
Tastes Like Diabetes: The third ending. In addition to having the casts' chibified heads floating around, it also includes dancing shikigami.
Too Cool to Live: Gen Shisho, Most of Kokuborou, especially Gagin and Kaguro, Mudou and Koya And most of the higher ups of the Shadow Organization.
Viewer Gender Confusion: The gender confusion over Madarao because he used Japanese feminine pronouns was bad enough that the creator had to step in and set things straight for the readers. The translators of the official English publication of the manga were the biggest victims.
He uses Japanese feminine pronouns in the original manga. In translations and the anime it's clear he's a guy.
The mangaka originally intended for Madarao to be female, but she never specifically said so and the anime used a male seiyuu. So she went with it and Madarao is now officially male.
Actually, an omake the author revealed that he was intended from the beginning to be gay
There was some confusion over Okuni, a member of the Urukai council who was clothed head to toe and switched gender pronouns at least three times over the course of the fan translations she was eventually confirmed to be female in the official one.
In Sen's first background appearance, before it was revealed he was a male, a number of readers assumed that he was female because the Dude Looks Like a Lady.