Between the loooong loading times and not even being able to retrieve the character list the STO experience has been frustrating.
This problem however is really annoying.
Finish a mission, exit the sector and the mission log still has it registered as incomplete.
It was at first suggested to me to "hail starfleet" to turn your mission in.
HA! It has to be complete first before you can "turn it in."
So once again I say riddle me that Cryptic.
Happened to me as well. I went back into the system (mission area), repeated everything and finally got it marked as completed. I think client/server comm is not very reliable, and from time to time, it's loosing info.