Because we, as human beings, are not responsible for our thoughts and feelings. You can't help that you feel in a specific way, or have a specific thought - even if that thought is intrusive or terrible. That's fine, that's normal, and it doesn't mean you are terrible for having a thought. It's only when you decide to act on those thoughts then we have a problem.
What I described now is how people act normally: but when they experience something traumatic, these thoughts get ten times worse. That's because our brains aren't wired to handle this kind of trauma so when it happens they react in weird ways, creating coping mechanisms that are almost always unhealthy and counter-productive. For an example look at all those stories of survivors who endured something terrible and then think it was all their fault, even though it obviously wasn't - that's their brain creating a coping mechanism to try to rationalize how something so terrible could have happened. This is what happened to Melrondia: she lost her sister, so her brain decided that instead of trying to process the loss it will sideline it and focus on the guy she had a puppy crush on and who is now free. These kind of "inappropriate" reactions to trauma often happen in real world as well and people who experience them often feel extremely guilty afterwards because they feel like they're terrible for having this kind of thoughts. Survivor guilt is a terrible experience that often takes years to unpack: It's actually a very well done and realistic representation.
What Melrondia and Gettemhart needed was healthy support groups that would allow them to slowly get over the trauma in an understanding and constructive way. ARKS clearly never heard of therapists - a group of friends can also be such a group but unfortunately they didn't have any except Zeno and each other. You can't help others if you're hurt yourself, so their dysfunctional relationship only made things worse over time, not better.
Melrondia eventually gets better because she gets seperated from a bad influence on her mental state (Gettemhart, and yes she is also a bad influence on him but that's neither one's fault - though you could make a point about how Gettemhart's side of the trauma is much more poorly written in a stereotypical manpain way, but we're getting distracted here), but also because she gets support in the form of someone who can hear her out and understand without judgement. In other words, the player character.
That was my tl;dr about basics of psychology and human empathy.
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