I got stuck in the TFO, and managed to fix it. I flew next to the transport ship that was bugging out, let myself die, and my warp core breach took the bugged transport out with me allowing the TFO to continue. Not ideal, but it fixes the problem. Also, the daily free phoenix box isn't working for me. Tried it in both DS9…
I've heard Kael address this exact issue in a live stream, and his response was that as much as they might like to give role-players a mission that "rewards diplomacy", it's hard to think of any way to do that without attracting a million min-maxers ready to exploit the optimal path through the dialog tree that they can…