Just stumbled upon this bug while questing in Silithus.
There are 2 quests that require the same thing: 1x Abyssal Scepter: https://tbc.wowhead.com/quest=9248/a-humble-offering and https://tbc.wowhead.com/quest=8352/scepter-of-the-council .
After turning in one of them, while having only 1 scepter in bags, the other one did not remove the yellow question mark on the map. The blizzard quest tracker updated correctly to 0/1.

@Cabro is this still an issue after so many commits addressing this?

I am not sure, this is one of the cases that has to be tested.

I've just tested this one with the exact quests listed and can confirm it's behaving normally now.