*Sigh* This is old news...
Question, did you delete or move all your old saves and persistent file before you did your run through? And not just the one in your game folder. You need to delete or move the ones that are in your user/app-data file as well. The persistent file retains all the choices you made in past play throughs. That could cause things not to route properly on repeated play throughs.
That being said, I'm aware there are massive inconsistencies in some of the girl's paths. There are a couple of reasons for the inconsistencies.
While the story is still in development, if I'm error free for 99% of the players, I'm happy. I'm not going spend weeks developing and writing paths that only 1% would choose. Hell, I've been asked to have a celibate path.
I've always felt my time was better spent moving the story forward rather than catering to the lowest common denominator.
When writing and coding the story, my default is to assume the player wants every girl.

I mean, it is a harem AVN after all...
I then go back and add opt outs for the folks that don't want this or that girl. The thing you to bear in mind is some of the girls are integral to the story. Whether you want to fuck them or not they are still going to be in the story. So just because you don't like them, the best to hope for is you don't have to fuck them. They aren't going to go poof! I could do it that way, but people are going to miss big chunks of the story.
The other issue is I used a very poor method of coding when I was
teaching myself to code Ren'Py. It was not error proof when making choices. I later learned how to set flags, which is a much better way to do it. So, we're left with a mish mash of code. The only way to fix it, is to completely re-code it from the beginning. It's going to take months to do. I'm a one-man operation, so you can forget any further progress in the story while I sort it out.
I have stated numerous times that I'm making the conscious choice to not do mid game remasters, reboots, etc. I hate it when it happens in games that I play and don't want to do it to the folks that play this one. I will remaster the game once Chapter One is complete. You'll just have to endure the gaps until then or just fuck them all.
It would make my life would be easier if everyone did!
RFFR
Dima