I suspect this is a bug that i encountered the other day (just had time to sit down and write about it).
I set some Duty Officers on the shipboard Assignment "Re-Align the phaser banks" (not entirely sure that is the name unfortunately). It was a 4 hour mission (no clue what color it was as i did not notice colors until later) that had a reward of 50 or so skill points, about the same for bridge officer skill points, and lastly it gave a blue Mark 3 Disruptor Cannon (or Heavy Disruptor cannon, no logged in so I don't know for sure right now). It also required 3 tactical or security duty officers to attempt the mission.
What I think is the bug is that I got all the rewards including the blue cannon but the mission completed as a Failure. I would think that if the mission was failure I should not get the loot and skill point rewards like that. I have read that some missions are still a success even though they fail. I would not think that this was one of those missions, but maybe I am wrong.
I will be on the look out for the mission again and make sure to try and get the right name for it.