I have an issue along these lines, however the faction didn't surrender to me. I have scavenging almost maxed. I have a privateer-type Commander ship going around harrying enemy units and scavenging the ships I destroy. I did this to a Citizen transport that I found in transit, and captured it. I am now unable to select or move that ship, there doesn't appear to be any lost citizens in the Citizens screen, transferring the ones I could didn't help, and now my game is brought to a complete stop, unable to move forward until I reassign what I assume is still the enemy's citizen, which I'm unable to do... Is this just unrecoverable? I'm going to backtrack to my previous auto-save, but if possible I'd love to fix it somehow.