I always try to have all locations in mind that I can visit at any given moment (and if there's a reason for another visit), so with and in a game as huge as yours, some mistakes are bound to happen, but considering your game's scope, you didn't let much or anything serious slip through. Players like me, who scale the Tower of Ragnarok in your game a second time (just because it wasn't possible before to explore the boss room manually), tend to maneuver themselves into tricky situations (on purpose). :D