After abandoning my 15 hours save and starting a new save, went through 5 hours of unskippable cutscenes, and repeated testing, I think I figured it out.
When you fight any bosses, if you somehow end them before they enter their second phase, you might not end the fight properly. As in no cutscenes of you grabbing their weapon and stabbing them, no key item reward, map icon sometimes doesn't disappear, and the boss arena warns you that you are leaving the fight, as if you didn't finish it.
As for how you would end them before their second phase, I think that's more glitch. Some bosses occasionally don't enter the second phase for some reason. I also had 2 bosses instant killed before second phase somehow, one was with an arrow that somehow did a huge amount of damage(while they were in the air), allowing me to kill it with a heavy attack combo. The other just got stuck or something and I again somehow did a huge damage, killing it in two hits. (both cases the boss was already close to second phase)
This is a really impactful glitch. Could you guys add in a "checking if a boss is dead" step when we reload a game? I don't care if you respawn the boss when this is found or just flag it as killed correctly. Either way, JUST LET ME TICK IT OFF THE CHECK LIST!!!
Edit: Also, Sometimes when I reload an older manual save, the game just doesn't do it. It reloads for a while and drop me back to my most recent autosave