Foe Yay: Majima is obsessed about having Mikuro on his side, and forces him to kiss his foot.
Shion says that he hates Shukaido so much that when in front of him he feels like a girl in love.
Fridge Logic Okay, so we know the moonbase it continually resupplied by drones clandestinely sent to Earth. This must also be where they get the manga they're reading from.... but their race is only the size of a human's thumb. Are the drones shrinking the manga for them?
And what exactly were they going to do if they'd evacuated to Earth like Shion wanted? Hook up with The Littles?
Ho Yay / Foe Yay: Shion is obsessed with Gyokuran. All the girls noticed and say that Shion must be in love with him.
Purity Sue: In canon: Mokuren is seen as one by other people, due her beauty and her status of kiche. She's not, and she suffers for that.
Rape as Drama / Rape Is Love: Subverted? Whether what happened between Shion and Mokuren was rape is moot as everyone is an Unreliable Narrator due to unclear memories heavily influenced by emotions. It causes Big Drama and propels much of the plot though. Interpretations of "what happened" in order they appeared in the manga:
It was rape: Shion raped Mokuren. He hated her personality and wanted to destroy her pure reputation and Kiche Virgin Power.
It wasn't rape at all - This scene happened when Shion was locked up in JAIL. Mokuren got a key, and went in there with him specifically so they could do the deed. (Mokuren's POV)
It was rape anyway, because she was blackmailed (Shion's POV) but Mokuren is so pure that her Virgin Power doesn't disappear and she can love and forgive Shion, which makes it ok. Interpreted by everyone including Shion as Rape Is Love to their dismay.
Eventually everyone's memories more or less clear up. Looks like it wasn't rape since both genuinely love and want to be with each other. Shion however didnt realize that Mokuren's feelings were so simple, instead choosing to believe that he manipulated her into bed with blackmail. (which would make him a bastard) Mokuren was temporarily swayed by Peer Pressure to consider that maybe she was raped. But she wasn't. Probably? We hope.
an interpretation that Rape Is Love was played straight: Shion tells Mokuren that he loves her and wants her to prove herself by coming to see him in his confinement cell and if she does he will admit his fault and work with the others on the Moon Base. However, as Mokuren learns too late, he does not love her, which leads to her trying to resist his advances but failing. His real goal was to have his way with her in order to claim her virginity before Gyokuren, his bitter rival, and to remove her blessed status as a Kiches Sarjalian. So his rape was never about love. However, the manga does not fully subvert the trope because Shion does eventually fall in love with Mokuren and she continues to obsessively love him even after the rape. Although the rape itself is never truly romanticized, the repercussions are sort of swept under the rug.