Carbonite has a variety of glitches. The main one being log tracking. After a few minutes it will lose track of how many mobs you killed/items looted and will not mark those as complete. For instance you need 6 wolf meat. You may get stuck at 4 on the carbonite quest log even though you have all 6. Or say you have to kill troggs, it will say in your chat bar you killed 12 troggs but over in the quest tracking pane it will say 6/12 or 0/12.

This also happens with single pickup quests where you have to loot a chest or box or barrel!

I will try to update with screenshots as a reload fixes these issues for a short time and i just did a reload.