You are not alone on this, the FOMO on this game is insane mainly because of the way the upgrades work.
Having to find copies of items in areas that you can only go once over and over again suck the enjoyment out of it especially in the "high stakes" missions, at least they should mark every missable item in the map for those missions.
Some enemies even drop chests with items so if you are not aware you could lose some items because finished the missing too quickly or the item was dropped behind some pillar etc.
I could tolerate the loss of some runes and even some unique items but losing some of the other equipment can brick a build.
To this day i still didn't find the second copy of Bellara Concentration bow or Davrin Assan's Fury without having to resort to Isabella shop at the end of the game.
The end areas chests have random items, I've found some upgrades to my weapons in some of those chests, they aren't totally pointless.