1) The part about the entire class 1-4 engaged in
enjo kosai, instigated by their previous homeroom teacher, Hayama who himself was motivated by those "suspicious people" Azaka mentioned early on in the movie (in fact the reason why Hayama was teaching there was to provide him a chance to bring the girls out). Most were forced into this mess, but not all; in fact, according to Mikiya's findings, there were some who eagerly took the "job" up. In the novel, Azaka notes that the school has a stale, suffocating atmosphere and the strict rules imposed upon the students (remember, this is a convent school and one where those rich young ladies attend) that denies these teenagers from the usual pleasures of their youth contribute to their accumalating frustrations. Mikiya believed that Hayama and co had initally fixed their eyes on only one student but once they got a taste of playing with one of these prim and proper ojou-sama...
Tachibana was the last student in the class to fall, perhaps due to her own religious convictions. While the movie states that she was injected with drugs, the novel also implied that she might also have been raped and impregnated, most likely by Hayama himself to force her to submit. As stated in the movie, nobody offered to help her in her distress; in fact, her classmates were more worried about her pregnancy or her seeking aid from the nuns that ran the school, which in either case would blow everything up (and since this school runs on prestige, just imagine the social backslash should the media finds out that the girls of the rich and powerful are entertaining men as escorts or even possibly spreading their legs like street hookers). Also, in the novel Tachibana did not survive the fire; in fact, she set fire to the campus to commit suicide (Azaka was pretty pissed off by this. She felt Tachibana gave up too easily until Mikiya explained that, as a staunch Christian, there was no way that the poor girl could have taken her own life, given the religion's view on suicide, unless she had taken it as a form of penance for her and her classmates' sins).
All in all, it's very ugly business.
2) Kurokiri's past, his relationship with Ouji Misaya and his eventual end in the novel. The movie skipped his backstory, and the end result sort of makes him look like some bored villian or a mercenary wasting time around young women. In the novel Kurokiri is a victim of a fairy kidnapping, very much like those cases involving changelings. For his case, he somehow escaped (IIRC he managed killed the faeroe holding him) but the price was that he could no longer treated his memories as his own memories. To him, memories have became records, words stored in his mind but nothing that belongs to him. In a way, he is very much like a common PC. For example, in his own words, the reason why he could identify Azaka as Azaka is simply because she fits the "description" of the person known as "Kokuto Azaka". If there happens to be a third person present that fits the description stored in his mind more than Azaka herself, to Kurokiri, that third person is "Kokuto Azaka, not the real thing herself.
This effectively renders him no more than a mirror than reflects the inner wishes of those who interacts with him. Tachibana approached him with the thought of suicide, so he hinted to her that that would be the best way to solve her problems. Ouji, who was actually an adoptee that was seperated from her own brother, approached him, thinking that he was her brother, and Kurokiri, answering her inner thoughts, allowed her to propagate that delusion. You can say that in a way, he's like a wishing well, answering to the desires of the well-wisher.
Now, we all remember how Ouji Misaya (nicely voiced by Mizuki Nana =3) mentioned how she could empathize with Azaka's brother complex. The movie didn't follow up on that, but in the novel Misaya did have romantic thoughts towards Kurokiri, upon whom she imposed her delusions about brotherly love... ehem. But IIRC she herself had subconsciously realised her mistake but did not face the truth until Azaka defeated her in the duel. In the end, like a jilted lover, Misaya murdered Kurokiri, who managed to escape from Shiki, with a knife. The man died with a smile though, so I guess it's not a total bad end.