Seems to my deductive skills that the following;
When you complete a campain mission co-op, instead of completing it for the person who isn't the leader of the group, it copies it instead to everyone not leading the party.
This results in getting several copies of the same quest - to the point where I can't enter a specific "Planet" any more since it has so many quests it instantly crashes opun me attempting to enter it. (All because we tried to clear his missions in that system.)
And every time you try to complete one of these copies it counts towards the progression, thus we get 20 / 5 clues on our investigations log.
This said, I found a "fix"(?) for it - more or less, you simply have to go in single player and complete them from bottom to top - for example some place holder missions are called Campain.Missions.something_4.name ---- The last number before the .name is what mission number it is, so if you have 5x 3.name missions you need to complete those, get 5x 4.name quests then you get the 5.name quest to be able to complete it.
After doing this you get the quest completed, although, it will leave you with a ton of 5.name quests - each granting the completion bonus of fate etc.. Which is kinda an exploitable way to farm fate. --- Just a little heads up for you devs =)