Did you, by any "chance", happen to press 4 to respawn and load back while the boss was downed and killed?
If the boss is killed during loading, it counts as finished but doesn't go towards your quest count since the quest counts the kill and it doesn't happen whilst loading.
This is the only reason this ever happens to me usually which is why you should avoid pressing 4 when you see the boss are close to 20% depending on how fast your pc is.