Yes remember that game was written back in 2013 (then I coded it in 2014). During the long testing (lasted over 6 months!) there was a sort of "peaceful riot"
in forums because there was no possibility to save Chalassa in the original script.
So together with the writer I decided to change this, to offer the chance to save her, but of course this lead to other problem like the one you mentioned.
Live and learn they say! One thing I've learned is that despite how much people say it's unrealistic, I will go with bisexual characters in future games, especially when there are "so few" (like 4) romanceable