I think that scene can be pretty easily cleared up with some hand waving storytelling.I think this aspect needs to be redone a bit at a later date. I recall 1 save I was on the Charlotte and Kaylah path and I recall a scene where the MC told her she was going to out to spend the night with Kaylah she acted like it was nothing and no big deal. But she gets super jealous of that redhead friend.
MC chooses that he is interested in Charlotte's path pretty early on (after Lucy's choice) in the game. But very little has happened by the time Kayla propositions him the first time. The second time I think both MC and Charlotte are realizing there is something more there.
MC enters into a relationship with Kaylah and talks to Charlotte about it. Charlotte seems very impressed if you turned Kaylah down, but accepts the physical relationship. But then Kaylah seems like she is starting to catch feels for the MC. That's also around the time, if on Charlotte's path that she starts to realize there might be something more. I personally expect there will be a decision point if you are on both paths, where Charlotte will tell MC to decide. I would also suspect Kaylah, if she has got feelings, would also want the same decision, both for her and to not hurt Charlotte.