The issues with the staff and procedures bugged me a bit ... until I remembered this was a period piece and put in the time period it was ... things still were a little wobbly but not as much?

That aside, Kai's flat 'arc' and Aoi's arc both bugged me a hell of a lot for probably the same reasons you listed, I just couldn't put them into words before. IDK, the deaths bugged me, but I'm supposed to be in bed right now, not commenting on fic analysis XD