I'm pretty sure the match with Long Chen's brother just hasn't been implemented yet. Not exactly a flaw.
When does the game tell you that Ro Hyi is the Little Demon Queen? MC is only suspicious about their mask in their initial meeting but realizes something was truly wrong when they encounter the pile of corpses in the cave and sees Ro Hyi among the list of dead disciples. I might be misremembering this detail though, perhaps the game did namedrop her true identity.
If the game tells you that you can now challenge Long Wyoung, while you can't actually do so in the current build, then I would call that a (small) flaw in the current build, since that line could have just been commented out until it gets updated.
If you pass a check (INT iirc, but I'm not clicking through the whole game to make sure :p) with the correct degree of success, when she tries to convince MC to follow her to the cave, then MC lists several similarities between Ro Huy/Hyi and the "Mistress/Little Demon Queen" (e.g. androgynous, wears mask to hide deformed face, etc.). So that comparison strongly suggests to me that MC recognizes her suspects her identity.
