After first logging into the game after today's patch, I actually had two separate missions titled "Welcoming the Federation" I entered the Expanse and a counter of 0/25 Fed ships destroyed appeared. However, after killing all 25 the counter disappeared and the mission did not complete. I attempted to zone out and then back in with no success, I then tried to drop the mission and reaquire it.
At this point the mission simply says "Defeat the Federation Fleet in the Kahless Expanse" with no counter. I have since destroyed over 100 ships in 3 different zones with no completion.