There are times when even talking to SF wont work or even going to the dude in person. >.< i just end up droping it bc there is alot more that will work for you and no resson to sit around trying to get it to work.
Actually I've run into several problems where I will complete a mission objective but it won't count.
For instance, I have several different missions that say "Win 3 Hostile Engagements or House Battles" (and another one that wants me to win 5 of them....as you can see Klingons are just LOADED with content =P). But I'll win one, and it will only count for one mission (and no, it does not specify ground or space).
I also noticed with the War Zone (where you fight the borg) I'm almost positive I've won it before (at least progressed through all the steps and had it reset) yet it won't give me credit for "Winning a War Zone". I figured I was just doing it wrong, but the PvP missions make me want to pull my hair out.