It appears that the captives disappear after capturing freighters and passenger liners. I just captured a freighter and the game said my shock troops returned with 97 captives. My security officer claims there are no captives on board, however, and when I do a personnel beam transfer, neither the freighter nor my ship show any captives.

My save files are available from Google Drive by the link below. My battlecruiser is in orbit with the freighter that I have just taken.

https://drive.google.com/file/d/1qQJkEdoCIhlD7elmFe1G0wbztO-fPTxZ/view?usp=sharing

Thanks!

Eric