We have no idea.
If you fingered Chika, i.e. saw the event Schadenfreude, before the beach trip where Rin confessed, you are a bad homie for breaking your promise to Rin to not pursue Chika before Rin had the chance to confess (made in the event Cafe Mocha), and Rin will give you shit about it for the rest of the game and not trust you as much (resulting in missing two events). If you didn't, you are a good homie.
Probably some childhood trauma we don't know about.
They are unavailable.
Missing events just means you don't see certain content on that playthrough. Some events are more impactful than others; Prisoner, though, is an awkward one to miss, because it's a huge component of two characters' storylines.