But if that conversation was about them feeling something for the same person, what reason does Jill have to suspect that that is what's happening here? Whether the MC is on close terms with Bella or not, there is no real indication for Jill to believe that there could be something between them or even that Bella likes him in that way. On the Bella path, Jill is surprised that she's warmed up to him so much and if you stay with her then you play Bella's favourite song on the guitar which shows signs of a closeness, but the conversation in the bed happens on every path including the one where Bella doesn't like the MC very much. In both cases, there's very little for Jill to go on that would make her suspicious of anything.
Then there's the question of who this person would have been and when did it happen. Did Jill have a thing for Bella's husband? Did Bella have something for another student while still married or after her husband left? Was it even a student or was it maybe someone older than Jill? It feels to me that this theory of them both once feeling something for the same person before has quite a few holes in it from both a character and narrative standpoint, moreso than some would say that the Jill/Bella "hook-up" theory has.
With regards to the Jill/Bella "hook-up" theory, if it was just a singular make-out session due to them both feeling emotionally vulnerable (my working hypothesis), that doesn't exactly rise to the level of "affair". It would have just been a one-time thing that likely happened in similar circumstances (being in bed together) that the two of them simply brushed off as a mistake and agreed not to let it happen. It's not like Good Girl Gone Bad where one sapphic kiss between friends can lead to them going from straight to gay. It could just have been one-and-done, and there was nothing more to it.
But then again, even if there was more to it, would it really be all that bad? Not saying "more" as in they did more than just kiss, it could still have been just a one-time kiss, but maybe it was more enjoyable than either of them have cared to admit and they're simply repressing it. Jill may come across as a sweet, innocent, and somewhat naive person who lives in a privileged bubble, but we've also seen signs that she may be sexually repressed. So moments of physical intimacy might awaken things in her and perhaps she wanted to carry on with Bella but she shut her down and straightened (no pun intended) her out. They moved past it for the sake of their friendship, but in moments like the one in ep 5 it resurfaces because it's not completely forgotten.
In any case, I hope we'll get some answers in ep 6 to this mystery and won't be left hanging too long because it was such a tease and probably the biggest "wait, wut?" moment since the end of ep 3.