I am currently replaying the game following an optimized save and I noticed 2 bugs.
1) In the Eustrin and Aram section of chapter 3, you do not need to "Talk to Mestan at the Main Stairs' Base" before you can "Talk with the Ivalan Priestess". (they share the same requirement switch in the code 1590 [Mestan Done].
2) In the tower of mist infiltration section, you can check "Take the Middle Chest Inside 2nd Floor Storage Room" whilst having 0 infiltration score despite needing to have at least 1 point to reach the chest (and getting another for opening it).
Maybe replace the tower of mist infiltration score, with "non-elite fights" and "storage room chests opened" with the option for the middle chest being locked behind "storage room chest opened"
Or at least make it so that checking the middle chest box sets your score to a minimum of 2