I chose to talk Audra down in the first companion quest and leave the transport untouched, but the quest reactivity acted like I had blown up the transport and the rest of the cell members were culled by the Protectorate.

I'm not sure if this was triggered because I killed the guards outside the transport before rescuing her or not, but that was not mentioned as having potential consequences. Likewise, on a previous playthrough, I had killed the guards and helped her blow up the transport and that did not cause the cell to be culled.

Same issue here, after talking her out of it, I used leadership to convince Niles not to blow it up either, and it's acting like I did the opposite.