I'm fairly certain that this is a case of three timelines. It's the only way that things would make sense. The first timeline is the original, in which the heroine had a VERY strong impression that the mc liked the class rep. In this timeline, the heroine had the exact same plan as the mc, which is to pretend like her feelings don't exist but in this case so that the mc doesn't fall in love with her and end up with the class rep instead. This is the only logical explanation as to why she would have such a strong reaction to the mc confessing to her at the end. She's not angry at the mc but angry at herself for messing up at the last step when every one of her friends were supposed to move on happily ever after. The third timeline is when the mc goes back in time. The mc should be going back to the original timeline where the heroine hasn't regressed in time. She isn't in her third loop, instead she's in her original state and the inconsistencies that she had is exactly because she didn't have the benefit of foresight. This timeline kind of shows up why she might've thought that the mc liked the class rep, and it really might've been the case that the mc originally liked the class rep in the first timeline. That's why the heroine was shocked and angry that she ended up inadvertently changing the mc's future "for the worse" by making him like her back in her second loop. Now in this third timeline, which is the ending we've seen, the mc returns to the original timeline finds the resolution where both of them can move on without strong regrets, and it's one where they end up having to hide their feelings from each other.
I think this theory makes sense and kind of salvages this manga for me, but honestly it was really quite the hectic writing near the end. Even if by some miracle I managed to the hit right on the nail with this theory, that would still be a minus from this manga's rating in my opinion because they clearly could've portrayed it a lot better instead of such a hectic ending. Even if we ignore the fact that they clearly planned to explore more about the heroine's point of view, they still set up so many things that they did not have the time to finish like apparently how the drummer gets hurt or they get dragged into the bassist's family troubles, not to mention how the class rep liked the mc. Given maybe one or two more volumes this would've been quite a decent manga but unfortunately it looks like they got axed and had to rush it so at the end of the day, I really can't hold it against them. Such a shame but it is what it is.