I have noticed while doing the standard "Patrol Sector" missions, sometimes the mission is not completing and being cleared off my list. The pattern seems to be if you enter a sector on patrol, and auto join an instance as you zone in, if you were not zoned in before the first objective was completed, the mission will not get flagged as complete.
Your mission entails patrolling sector X and defeating 5 enemy squadrons while there.
1. You zone into sector X.
2. As you zone in, you are auto teamed joining other players already in the instance.
3. If the other players defeated the first enemy squadron before you zoned in, the mission will not complete for you and you have to redo it.
This does not happen all the time, yet it is frequent enough that it warrants a look.