So annoyed with this game in that if you don't do things a certain way you are basically stuck and cannot progress and simply must reload the last save by exiting to the main menu (the only way).
Alignment Control area when you go down the lift platform in Koboh:
YFor me the trigger does not happen and the enemies do not enter through the currently locked doorway. I youtubed it and for others that doorway is a trigger point which openes it up and you battle them, yet for me I must have missed doing something before entering that area and now the trigger never happens. It's not a main objective area so won't break progress, but it is a side mission that I can now no longer do for whatever reason
Moldy Depths:
Another side mission in Koboh, you MUST enter the cave with a Nekko, if you do not then you simply cannot escape once in there as there is a platform of height that only a Nekko jump allows you to reach. Again, must exit to main menu and reload the last save which might be a distance away
Those are the immediate two off the top of my head so bound to be others.