I think I may have a line on what is causing the problem. And also why another issue I noticed but thought might just be my misunderstanding of the mission parameters. While running around hunting council in Bricktown I noticed the counter did not tic down every time I took one out. Sometimes it would, but not always.
Tonight, while doing another council hunting mission in Founder's Falls, I noticed that there was a mixture of mobs with the same uniforms and titles but some with the faction "Council" while others had the faction "5th Column", a name I had not seen since I started playing the game shortly after release. (I think 5th C was removed from the game waaay back shortly after release because they were based upon the Nazi's and NCsoft wanted to sell the game in Germany and all references to Nazi's and their symbols are forbidden by law.)
While I have no problem with 5th column myself, as bad guys to whip, since Nazi's have always been great villains to beat on in stories of all types, but having mobs from an unrecognized factions could cause some anomalous behavior. I actually saw some members of the same spawn fighting one another, some from Council and others 5th C.
Just a thought.
Oh, and thanks for the game. Have enjoyed my time back quite a bit.