Jeremy only knows if Lena fucked Axel if she does it at the club where he works. His co-worker Marcel catches you there literally in middle of the act with Axel's cock up your Lena's snatch. Guess what, people gossip with co-workers.I may do some serious backtracking through the variables in the game to see what exactly you have to do, but this is REALLY messed up. How Minerva plays a part when NOBODY KNOWS IAN IS SLEEPING WITH HER is beyond my comprehension, or how ANYONE knows that Lena slept with Axel?! Yet in my current playthrough (which is basically, everyone's a whore, LOL) somehow, Jeremy knows that Lena slept with Axel even though niether Lena nor Axel told anyone, and I still don't see the logic on how that remotely effects a threesome with Ian, Lena and Holly, if anything it makes her more open to doing anyone and everyone.
As for the throuple, it's not just some sort of casual threesome. This path is for Lena and Ian who love each other (and both have feelings for Holly) and don't get distracted by hookups with other people. If either Ian or Lena sleeps around with other people or especially if they develop feelings for other people, like Lena can with Axel if you choose for her to sleep with him repeatedly, then they lack feelings/commitment for this "pure" throuple.
It's not exactly rocket science, when both protagonists repeatedly spell out their thoughts on the matter in their internal monologues.