It may be that you triggered some out of order? Don't know about that. Decided to do a second play-through from the beginning, and corrected the scenes I missed last time, since I just explored (did not give Wilson Priti's pics the first time through, or show Lucy my dick). I did NOT manage to get Emily's skirt, part 2; I think I passed another rule at the same time as the one that triggers this scene, and enforcing it first makes her wear regulation panties. Ah well, maybe next time.
On Rachel, I have not finished her yet on second pass, but I did notice that because I did the Volleyball Keys quest very late, I got the sex with Sally scene immediately after the Rachel and Sally share with boobs scene, and as a result, Rachel did not appear for punishment, and when summoned, I did not get the updated options (have not caught her misbehaving since, we'll see). On the first play-through, a trigger like that happened on the Old Headmaster emails: I read them before their step was triggered, then had to do it again afterwards. Might be similar here: check the scene replay menu and see if there is a locked one for Rachel that happens before one you have finished, and do those: I currently have Trouble in the Showers unlocked but 5 scenes before that are still locked, and I expect that I'll need to finish those before Rachel actually appears for the punishment described above. I think 4 are probably playtime scenes, maybe all five, but since I have Trouble in the Showers unlocked, the Quest Log says put the dildo in her rear, even though I haven't unlocked the move through play. Maybe you are in a similar spot.
I also let Rachel win her online fight on the first time through this time (by only distracting once) to see what would happen. However, she practicing the splits now when I spy because the shower thing happened the next day. Curious to see how this works out.