Jestur I think I have found more problems with the girls' routes. After deciding not to risk my relationship with Jessica, on leaving the room with Skylar I saw the text saying that we cleaned ourselves up and got dressed. But that should only happen if you risk your relationship, leading to fun times with Skylar. I filed that away to look into later.
Then when she texts you about her mom after you met, she says she thinks you should cancel the planned date. Also only something that was happening if you decide to risk your relationship with Jessica.
I installed the RenPy dev tools to see what's going on.
I found two sets of route stats tracking whether you're on someone's route. E.g., 'jessicaRoute' (currently True) and 'routeStatusJes' (currently "Not on route'). The second is what's showing on the phone. The same pair for Alyssa and Jenny are also "True" and "Not on route".
Skylar's are 'True' and '?'. While the phone uses routeStatusSky, the code is checking skylarRoute for those bits of description and dialogue. Therefore showing me what I would see if I was on her route when it shouldn't.
Presumably one of these variables should be discarded. Tracking essentially the same thing in multiple variables is complicated and can easily lead to this kind of problem. There are ways to design code that will handle it correctly, but that requires coordination through shared methods and not directly updating individual variables. The simpler method is to have only one variable tracking this status.
Because RenPy seems to break saves really easily, I suspect that setting skylarRoute to False in that bedroom conversation will be a problem, but my RenPy knowledge is limited. You'd have to add a new line to the code and I fear that will mean all saves after will be unable to find the correct line on which they were saved. But if you stop using the xRoute vars and only use routeStatusX, you'd probably be fine. Or if you feel you need both, maybe you could replace both with a class and have a method which updates both at the same time. You know more here than I do, so do whatever works and doesn't break saves (unless you have no choice).
I'm nearing the end of episode 3, after which I will be in unfamiliar territory. Looking forward to it!