I think it's kind of weird that neither Ibuki or Saionji seem to have any hard feelings about being killed by Mikan. Granted, Mikan wasn't exactly in control (though her calling out everyone for not stopping the bullying and just standing there may be repressed frustration and resentment) at the time and Ibuki doesn't seem to be the grudge holding type but I wouldve expected Saionji to hate her even more and use it as an excuse to hassle her even more.
We don't really know how long before the "Hope Side" episode they actually all woke up. I suppose that, based on the emails we see from the Future Foundation higher-ups to Naegi and company in the final chapter of DR2, it couldn't have been very long between the end of DR2 and the start of DR3. But even if it was just one week at the most... maybe they've been dealing with this emotional baggage back on Jabberwock. Maybe they worked through things back there. Idk.
Even if they did wake up only shortly before they headed for the Future Foundation's HQ, we don't get much insight into how they feel once they're up and about. We've only seen one half-hour anime episode which contains each DR2 character for like, a few minutes each. And during those minutes, they spend a decent amount focused on the task at hand - that is, stopping Mitarai's broadcast. So we really don't know much about how they actually feel. .... Although I admit that when we do see them outside of "combat mode," they sure seem like they're getting along.
I mean... that COULD be Ibuki letting out some kind of rant while Mikan is listening with concern, but I highly doubt it.
But even if they're looking to be hunky-dory by the end of DR3, who knows what they might be dealing with under the surface, y'know? It might feel great to have all your memories of your original friendships back and be totally reunited in the moment, but that doesn't mean they aren't going to have simmering resentment once they get over that initial high.
My last thought is that this should logically apply to Mahiru and Peko, too. AND the entire group should rightly feel pretty salty about Komaeda's behavior across Chapters 4-5, especially his actions in Chapter 5. Although I guess I already kind of wrote a fic about that.
Anyway, my point is: I think they've most likely got a lot to work through... or that they could've started working through already? But yeah, I do foresee some baggage there. And I most definitely wouldn't put it past Hiyoko to be nursing a grudge.
................................but idk if Ibuki is even capable of "hard feelings," frankly. She seems very live-and-let-live.
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Mikan: "Um... Mioda-san? I just wa-wanted to say that... I'm... well, I-I'm really, REALLY sorry about—"
Ibuki: *interrupting* "Don't even worry 'bout it! 'sall good, babygirl!"
Mikan: *blinks* "...eh?!?!"
Ibuki: "Oh, I mean I don't have any hard feelings! Didn't even particularly mind gettin' strangled." *shrugs* "It's whatever. You get me?"
Mikan: *bewildered*"...................................thaaaaa... thank you, I-I think???"