That was a problem the show had a bunch over the course of it's run. The shows concept would have worked much better if it was semi-serialized. Like, still have weekly storylines, but let some things carry over several episodes. It was ridiculous how the end of one episode would have the ship on the verge of destruction and the next week it was as good as new.
I remember reading that the year of hell was originally conceived as a season long storyline. But the showrunner or one of the producers refused to allow it.