I stood there for 10 seconds while checking a email because the animation of opening that chest is already long enough, then after I checked my email and looked up, there was a distinct lack of opened chest on my screen. So I waited for another 10 seconds, before fetching my keyboard and recorded this video

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

I killed Cordelia in Berkelow Bog, but no cutscene or item received popup appeared. When I tried to leave, it says

"You are leaving the fight area"

as if I didn't finish the fight.

I killed the other two prior to this so I went to the statue with 3 slits, no cutscene either.

I stood there for 10 seconds while checking a email because the animation of opening that chest is already long enough, then after I checked my email and looked up, there was a distinct lack of opened chest on my screen. So I waited for another 10 seconds, before fetching my keyboard and recorded this video

@ronin-8654 same here. tried a bunch of way to get over it but I wondered too long and my last auto save is now right after I picked up the nonexisting key

During the quest "Ever As Fate Must", at one point in the cave exploration, I slide down a hill, land in a "cursed" area, where there's a locked door, a key and a skull that seem to be source of the curse. I went to pick up the key, turned around, destroyed the skull. And walked toward the locked door, which says "you need a key to open this, go find a key". I checked again, the key isn't in my inventory nor is it still on the stone I picked up from.
My oldest save is the exact moment I picked up the key and destroyed the skull. I know this because when I reload that save, my character immediately says "but what good is a key without a lock."