They are broken because people think they should be able to do all the content, independent of how they aproach it.
Take the undercity for example, if you follow the quest line that takes you to the gullet, coming from the palace, with the queens brother quest to investigate, then it all works out fine... You go there, you talk around, find a way to the black market, find a way to doreo, he gives you the conch, you go down with the elevator, talk to the pirates, follow your contact to the undercity, find the other conch, then are able to explore the locked room.
If you go directly to the gullet, talk to the guard to let you down there, without the context of what you should be doing down there (lore about the lost island), barge into the pirates in a way that doesnt take you directly to their leader (fail to use stealth), then the entire thing feels incomplete.
Game is built with a particular order of content in mind, and it gives you cues to follow it, if you go mucking about out of that order, then some content might not work as intended.