I'm a librarian who loves anime, manga, and reading a wide variety of genres.
At some point in this story, Phoenix and his team got to know Dakota well enough to sit with her and comfort her as she tried to deal with the realization that she's just a computer program (not really a spoiler since they've all referred to themselves as NPCs since the beginning).
The problem: readers weren't invited to any of that. We somehow jumped from Phoenix finding Dakota's freakouts during battle annoying to Dakota learning how to fit in more with the team without any of it ever showing up on-page. As a result, this whole crying and hugging scene just comes across as weird and out-of-character.