I finished both these patrols last night and it said mission completed depart system. After I have departed the system the quests still show in my log and when I hail Starfleet they do not count as done! Am I doing something wrong or is this a bug?
I have the same "bug". I have done the Kinjer mission 2 times and I complete it but when I get back to sector space it still does not update and I if I enter the system again I get the mission over and over again. It's not possible to complete it!! what to do?
One workaround, certainly for the Kinjer mission, is to save those specific systems until last. When you have completed the final mission, DON'T warp out to sector but hail Starfleet whilst still in system and hand in the quest then. All things being well, it should give you credit for it and allow you to hand in there.
I believe this should work for other systems with the same bug where credit is not given for completing a patrol mission.