The Isabelle walking in was never actually shown, it appears to be something that will be added later on (likely a slight retcon of Dethroning the Queen quest where if you choose to fuck Kate, Isabelle will walk in). It's weird rn because she never does walk in, and on my main file, I ain't even fuck Kate at all, and the quest still says I did.
Incorrect.
While, it's true that she won't walk in on you if you choose "Maybe, but I want a turn with the mask." (she'll stay to clean up and then wait for you in the cafeteria), if you choose either of the other options, and you let Isabelle convince you to continue, you'll tell her to go get the key, and she will walk in on you at the very end of it. (This is true even before 1.40, tested on 1.39)
The real "problem" is that the new quest says she did walk in on us even if she didn't, and as you said, even if it never happened. I say "problem" in quotation because the
reason is that the quest is WIP, and, when it's finished, will probably be either completely different, or not activate at all, if she didn't walk in on us.
... And I say "probably", because in the Flora quest "Squid Game" there's a line of dialogue that refers to something that never happened if you're doing the love route, but that's much less of an oversight than an entire
quest revolving around something that never happened.