I have done a few of these sort of missions and if you look in your transactions tab, the mission should update with how many of the targets you've destroyed, but have also noticed it not showing up. Could be server not updating it quickly or just a bug.
[EDIT] sorry just skimmed it, I never noticed the text that said to pull them out of SC, I think that's what I was doing though.
But thats the problem. At no point in the mission brief did it specify. And there was no updates on the transactions tab, no count. I ignored the alt ending to the mission and continued hunting.
The game just assumes you know all these things, when really the mission brief should state it needed to be done in super cruise and that hey, you dont have an interdicter but will need one to complete it.
Its like I read that for the pirate version you need to be in USS. Which again, basing the outcome via RNG seems to be bad design decisions.
So traders are in supercruise, pirates are in uss. Why cant both count?
Too much disorganization within the missions.