Now I am slowly leveling my toon today and encountered four missions today which I can not complete in some shap or form since the last patch last night. I don't remember the details of the earlier two misisons but when four of the six missions I attempt are bugged something is seriously wrong.
Patrol Tenebia sector - incompleable due to inablity to complete patrol Elvren sector simply cause mission doesn't update completed when you scan the final node.
Under the cover of night- incompletable as the mission doesn't complete after you capture Franklin Drake and beam back up to your ship and fight off the romulans in space. beams you back out to the sector map and doesn't complete the mission.
There was an earlier escort mission where you have to protect a frieghter, and it gets attacked only problem is the frieghter stops moving and nothing happens for several minutes, after a while the ambushes finally spawn in and attack you. I was eventually able to complete this one by just sitting around for ten minutes for the ambushes to spawn in.
Another mission you have to protect a disabled ship from waves of attack, the final wave of attack the ship is in cloaked mode and just flies around. You can see the ship is near by when you target the disabled ship as it has the cloaked ship targetted and you can only fire on this cloaked ship is you happen to be near enough to it that you see through its cloak to shoot it. This final cloaked ship took 5 to 10 minutes to kill due to this bug rather than the 30-60 seconds it used to take.
Right now I am far from happy with the quality of the quality control in this game.
While it's a PITA, there is a workaround that has worked for me 100% of the time when a mission hasn't updated in a chain, as you described. I simply move on to another mission, or go to ESD, or do something for about ten to fifteen minutes. That allows the server to "reboot" and remove the instance you were in at the time of the error. Reenter the system, and redo that portion, and it should update correctly when complete. It has always worked for me, even before season 4 when it became an epidemic. Good luck!
I had the Drake bug. The way I got around it was changing where I encountered him. Every time I encountered him at the buildings on the top left of the beam in spot at the top of the hill the game was bugged - he would not beam out. When I reset and changed my patrol pattern so that he was encountered in what would normally be the first set of buildings I'd go to he beamed out fine. That was after 3 retries.
They do have a ticket on that mission, from me for sure, so hopefully it'll get fixed soon.