Well, I guess I haven't encountered these bugs because I've been dilly-dallying around the prison and not doing any main quests😅
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Well, there are some quests that you have to start in order to finish others, but I guess if you're not doing any of them then none of them are prerequisites for continuing to do none of them.
I guess it's true that most of the bugs have to do with specific questlines, and they could theoretically just be incomplete... but if that is the case then they've been left off at an incredibly weird spot rather than a reasonable cutoff point.