I haven't seen this mentioned, but there is something I noticed. This is just guess work right now as I still need to test it. But I think having Unlimited Use Consumables or Obtain All Skill Cards on, breaks being able to get certain items. Essentially it seems to break being able to get items for Elizabeth's requests. The characters who you get the items from never seems to get the prompt to give me the item. I'm guessing it's because the code of the game thinks I have the item already even though I don't. If anybody has used these options but have not had the issue then please let me know. For now I'm going to try and test my theory.
Working off of a new save, it seems like 'Easy Open Chests' might be the culprit? The only cheats I have used so far on this save is the HP, MP and Easy Open Chests. I doubt it HP or MP since that doesn't touch inventory. There are random items that I just have 99 of. These are items I've never bought. I got one as a reward after a fight or opening a chest. No clue if this breaks some of the requests though. It takes a bit to unlock that part of the game.