Tried it again today. Appearently the 3rd wave of Klingon ships now consists of only 1 Raptor class vessel, no BoPs. And destroying this one ship does not count as separate wave meaning you'll end up with 4 out of 5 waves at the end. It can't be completed at least not for me...
This bug wouldn't bother me at all, if it weren't that beta Thoridar is one of the systems for the radiation scan satellite mission too, so everyday I finish 4/5 waves, get the satellite then have to do one extra system to finish the patrol mission.
The issue might be related to the addition/renaming of Hegh'ta Heavy BoP's. Beta Thoridor's 3rd wave can spawn either a Raptor or Vor'cha, then either a BoP and three fighters or five fighters. (This is my most common experience.)
Note the BoP. It is a plain 'Bird of Prey.' When all the others that spawn in the other waves are either Hegh'tas or the other named type. (Ki'tangs or B'rels, I forget at the moment.)
Before LoR this was fine. However it seems that the Patrol was changed to only count named BoP's and the spawns updated to carry those. This 3rd wave seem to have missed that spawn update and so the patrol becomes impossible to complete because it doesn't count that BoP.
Confirmed and filed a bug report for it the other day.
I've gotten mixed results.. being able to clear it some times and other times not - generally because a spawn doesn't happen.
My personal guess is that there is something wrong with the Klingon spawn tables. With the Patrols there's a chance of a science/support ship sometimes spawning instead of the regular escort/destroyer. Perhaps the wave is trying to spawn a ship that doesn't exist/isn't properly referenced?