I'm a new player and wanted to see how it worked to capture someone who came to "visit" my colony. Upon capturing them, as expected, their entire colony became my enemy. I then loaded a save from about 30 seconds before the capture order was executed (created when the visitor was still "blue" and his faction still friendly to me). Upon the load completing, and prior to the "arrest" order being executed (though it was queued to happen, and was in the save state for the loaded game) the visitor was now tagged as an enemy and attacked my colony, and in the overview window the damage done to faction relations had persisted as well.
Yeah that is very upsetting, on A8 still happens hope gets fixed soon :D
Reopened bug report on Mantis: https://ludeon.com/mantis/view.php?id=1403