I think you nail it. The problem with the situation bows down to three points:
1 - The MC wants an harem, which means that turned out okay even if in a extremely anti-climatic way.
2 - The MC only cares about 1 of them, meaning the situation is awfully dealt with. A "what about me? this isn't just about you!" situation and that talk NEVER HAPPENS!
3 - The MC doesn't care about neither of them, which was also okay considering them just friends but I understand people giving 0 shits about their relationship and others who wanted to tell to their faces to fuck off and get out the MC life.
Like in AL, I think PinkCake led himself into a corner by forcing the player into a 3 way relationship that many people simply didn't wanted (me personally, too), and he did it again in BADIK. From what I've seen, 90% of the people who roam around this forum didn't enjoyed how things were handled, one way or another. The biggest problem is that it seemed to be the focus of the game for so long, since the very start, honestly, that this episode should had been all focused on that, and it ends up being the MC sulking all episode long giving a silence treatment to Maya and Josy and then dealt with one very lousy conversation on how they are all lonely and hurt, that the "lies" was what mattered and not their feelings towards each other ater finding out there's another people that was there when the SO wasn't, THE MC. I think DPC forgot the MCs part in this emotional roolercooster and sold it too much that Maya and Josy are a thing, now and forever, with the MC being in... or out. It still blews my mind how Maya and Josy just got back together so easily after the whole season is about them being almost just about to break up.
So if you ask me, DPC mistake in this was giving what it felt like a big choice by the end of the season, he should let it play out for season 2 and Maya and Josy breaking up, or see other people, and slowly work with the MC to realise if they're going to get back together again (the result of the MC not caring OR caring for both of them), or the MC chooses one over the other. This might still happen but I think the main problem resides on the fact that one shippers got the end of the stick in this situation, either go harem or friendzone them, thats it.