The problem here is that MC is overly good to them even after friendzoning them. After kicking them to the curb, he's giving them the wrong impression and signal that he still cares, thus confusing them.
As I told someone before, there is no such thing as regarding a female as "friend" for a male, especially attractive ones. For a male to befriend a female, the female has to attract the male first for him to even consider it.
I am not sure about the culture in this game, but the relationship development from first met -> attracted -> sex -> break up -> get back together -> make up sex -> threesome in 2 weeks in warp speed in my books.
This "problem", I feel, is directly related to the way the game plays out and the overall arc of the story which in itself could be seen as a problem.
The issue is that there are all these choices where players can avoid interactions with pretty much every LI, and the assumption for some is that this means they can avoid these LIs in the future and/or that there are no feelings between them, but then the story shoehorns in feelings because, for reasons known only to DPC, it's important for the story. Well, if it was so important that these characters feel something for each other, then the build-up events shouldn't have been so easily avoidable.
Take Josy, for example; the player can say and do all the wrongs things that either give no points or negative points for her and can choose to leave after the date, but she'll still express deep feelings for the MC in ep 5 even though he's not been very good to her. Now, sometimes, in the real world, you can have an attraction to a person you know little to nothing about and who you haven't really spent any time with, so that could be what's happening here, but I would say that most people approach these games from the perspective of "more interactions = more feelings", and that not interacting with a LI should mean there are no feelings. For her to feel so strongly about him, she and the MC should have at least had some good interactions, but even on a totally anti-Josy path, she still likes him a lot which is strange.
This then makes the choices feel somewhat false because, even though it does lead to not being in intimate relationships with certain LIs, it doesn't impact the feelings the LIs have for the MC and vice-versa. It therefore causes confusion in players who have completely avoided certain LIs to have them suddenly express feelings and makes the game feel less like one where choices matter and more like a linear game with false choices because the characters are so important to the plot that they have to stay active and relevant in the MC's life even if players don't want them there.