There are 2 missions, Empire Defense Against Federation Spies and Empire Defense Against Federation Encroachment, that require 3 defeats of battle groups in the Kahless Expanse. However, when you defeat the required 9 battle groups it does not give credit towards both missions (I've had a few times when neither mission was credited). So instead of having to do this 3 times for both missions you have to do it 6 times.
I did report this as a bug in the game.
In addition, the enemies in this area don't scale to the player's level. They are all T1 (level 7-9) ships which provide no challenge and only drop white Mk II loot. Since I'm now using Mk IV loot this is all just vendor trash.
I just completed Empire Defense Against Federation Encroachment and picked it up again. My Empire Defense Against Federation Spies is at 2/3. When I killed off another battle group, it credited Empire Defense Against Federation Encroachment (so it's 1/3).
My guess is that it's only giving the credit based on alphabetical order, but who knows?
I'm am getting only about a 33% chance of the submission loading when I enter one of the anomalies. I can even leave the Kahless Expanse and come back in, scan on of the readings, enter the anomaly, kill the ships that immediately attack and nothing. No credit for the group kill because no mission loaded. Like I said this happens 2 out of 3 times. Anyone else experiencing this? Did report it as a bug.