Maybe I'm just unlucky, but since the patch these missions (at least the ones in Romulan-controlled sectors) either are close to unplayable or you don't get credit for completing them.
First issue: instantly "spawning" into a group of 12-15 romulans, 6 of them the big behemoths who just take turns one after the next hitting me with that stupid incapacitation purple beam and all shoot me until I'm dead. Wait for respawn - respawn in the *same* exact spot except all of the ROmulans are fully healed now (assuming I even got off any shots beofre I died) and repeat. Can't even try and warp out before it happens. Spent my first 20 minutes tonight in that endless cycle until enough other Feds came into the instance then after another 20 minutes we were able to finally start killing them one by one.
I completely agree with some Romulans spawning in the "spawn area" when the mission starts over, but not in-between while waiting for the timer cooldown to finish. Also, for the longest time *I* was the sole ship in this instance - without help there was no way I was going to ever end the viscious cycle I was caught in.
Second issue: some instances I'd complete, no more romulans left, but the respawn countdown timer never appeared. No more enemies, nothing, and no credit for completing the deep space encounter. And yes, I did bug this.
C'mon guys, played for over 90 minutes tonight with almost nothing to show for it but some dented keys on my keyboard from trying to get through the mindless death cycle I was in. Don't know what you changed, but it isn't working!