I & many others, who try to do every quest on a planet, has ran into the same issue: finishing a quest, only to later find out it was part of the "Bonus Series" quests, and now you can never finis the series. I see two fixes to this issue: 1- Only enable the quest when reaching a specific stage in the Bonus Series, or 2- Make it so that the "Quest Log" recognizes that the required quest is already done, and there for marking it as finished and progressing the Series. This is an issue, becuase unless you do proper research, you are discouraged to pick up "exploration quests" out of fear that it will later mess up a quest line/Bonus series.