Nostalrius Begins - Quality wow vanilla realm (1.12)

This happened to many players about 20 minutes ago. The server was reset and everything was rolled back a couple of minutes. Those of us who had just turned in quests when it happened, had the quest items taken away but quests was not registered as turned in when the server came back up.

Now the quests have a yellow question mark above the quest giver as if they were finished, but can't hand them in due to the missing quest items.

Any idea on how to fix this?

Abandon the quest and get it again and gather the quest item again. It sucks but that's the only thing you can do as far as I know.