Naegi as the only one who comes to Sayaka's defense when his classmates celebrate Sayaka's death.
Kyouko Kirigiri convincing her classmates that they're being dumbasses for pinning Sayaka's murder on Naegi.
Unlike in the game, here there's dialogue as Leon is being executed, and this time Naegi and Aoi acknowledge that they don't even know why they're watching something this brutal.
Oowada and Ishimaru's bromance.
There's something downright adorable about the way Asahina says "Kawa."
Similarly, the fact that Genocider Syo of all people has not one but two pet names for Naegi; Naegels and Nigel
Both Kirigiri and Monokuma refusing to call Fujisaki male (Monokuma specifically using they/their as a pronoun) after the revelation of Fujisaki's physical sex, because they weren't sure if Fujisaki was Transgender and didn't want to disrespect that if it were true. To quote Monokuma's sign:
Disclaimer: Though I enjoy watching high school students murder each other, people being offended by fictional characters is another thing altogether! That's why I am stating for the record that one's genitalia is not an indicator of their gender identity and I hope you do not believe otherwise! Thank you and goodnight!
Faulerro-as-Monokuma, in spite of ribbing on the English trailer, like how they actually SPOILED some major plot events... by the end of it, he still recommends everyone to support the release of Trigger Happy Havoc and to buy the game, since it'll be beneficial for the Western fanbase.