I'll take a look at this one more time. I may just have to make the transports unkillable after you loot them, as it's this logic that is the root cause of all the problems.
I didn't want to do this because I wanted to give you guys the option of blowing up the friegters after you looted them but at this point just pulling that option is the only way I think I can fix this issue for good.
TO CARRIER PILOTS:
The carrier problem does stem from lack of pet control, combined with pet AI going on a diehard vendetta is the need for finesse because if you get out too many squads they'll kill the freighter before you loot it despite it turning friendly torpedos en route destroy it. This mission was promised more optionals based on class, but they have yet to materialize.
Unkillable, no thanks. I am still wondering however if it is still counting dead freighters towards a fail like it was, because if four get away & two are destroyed before you finish scanning all four, then deaths counting towards failing the objective may still be the problem. Confirm I'm wrong then I'll leave you alone Gozer. Wait, one more thing when are we going to get those class based optionals on these? I'm tired of not getting it in my engineer cruiser because I can't AOE dmg as well as escorts or scis with grav. well.