The game gives you the player the ability to choose how events can play out. You failed or decided to ignore the warnings or requests or events within the game world, your decision/s have consequences. Just roll with it, the game isn't designed around or meant to be a series of sterile check boxes that you tick as you progress. It will not hold your hand and say you must do this or this will happen... but you can mitigate the possibility of poor outcomes by reviewing your quest log.
