So the Coil's of Bahamut are the level 50 raid series. You wouldnt see the quests for the 2nd and 3rd set of floors until you beat the first set of floors and associated quests. Each raid series is set up that way. The alexander and omega raid sets are something like 12 quests each, but you just see the first one. There are a few dungeons like that too. The side-story cant send you to arboretum hard if you never cleared arboretum. The allied beast tribe quests work that way. You have to finish faction with multiple tribes before the quest to bring them together against a common foe would make sense. And most later expansion zones have over-arching storylines. You might have to finish the story of 2 or 3 people/places for the final quests of the zone to show up.