So, I have been replaying this game with URM and I noticed a sort of plot hole :
If you tell Micaela that you have a crush on her in the past, she will react either positively or negatively depending on your affection score with her. But most of her affection points are gained in the present timeline. So basically if you're nicer to her in the present, she likes you more in the past, which doesn't make a whole lot of sense.
It's a relatively minor issue all things considered, but might become a bigger problem moving forward. Especially since the story is gonna go back and forth from past to present, it'd be a kind of temporal paradox.
I suppose one way to alleviate this problem would be to have two different affection value for each LI, one for past and one for present. For the flashback, only the past value is checked and for the present timeline, sum of both values are considered. But I guess it might be too much work for not a lot of payoff.