I was visiting Malignus, and I completed the protect-Darkeye-from-Cerzak battle during one of the trips. I had started the Darkeye mission, but not finished, and so came back to train some more. I decided to see if I could deal with the fight at the end of the mission, and when I talked to Gen. Tastidian, I found I had "completed" the mission. I could use the boat, find the yellow orb, dock on the Gen. Darkeye side, but the cave was empty. Pirate Pete never showed up, so I was disqualified for his orb.
The second one probably isn't a glitch, but I visited Malignus, and decided to see if I could do the Nelis mission solo. I succeeded, and won the game. I had just "completed" the Darkeye mission.