Iana wondering why Yomi (i think that's the prince's name) dislikes her even though she knows why and actively made those core memories that fuels Yomi's hatred for her even worse doesn't make sense either.
Yomi is the guy who was originally a villain who went after Konoha for revenge after Iana died. The prince is Ginoford.
She's not confused why he dislikes her, she's wondering why he seems to hate her to increasingly irrational degrees with every encounter even when she has not been actively doing things to worsen his impression of her.
Like, Yomi calls him out on flagrant hypocrisy for blaming her for other people's decision to
launch boulders at a police hospital when the "worst" thing she's recently done is reveal that one of the things she was accused of was the work of a different person. The two core memories are the death of his grandmother that hasn't been properly investigated and the incident where she took credit for Isaac's death, got shot, and awakened Konoha's saintess powers after much narrative delay.
Strong odds are this is something to do with the Dark History saying he's supposed to have been in a coma for months now, but time will tell.