This seems to be a common issue with games of this genre. I don't know if it's difficult to fix or just often overlooked due to the sheer number of possibilities, but it's extremely common that dialogue (especially dialogue that doesn't have any variables associated with it) will not at all reflect the actual state of the story. I don't necessarily mind this with repeatable dialogue that never changes, but when I'm encountering someone for the first time and they say something verifiably false or out of tune, that's a problem.