Bought a ship off the black market, got chased by a hegemony patrol. Turned my transponder off before exiting the system and got intercepted by the patrol in hyperspace, who then demanded I turn my transponder back on and submit to a scan. After the scan was over I immediately got the "You match the profile of a suspected smuggler" dialogue and was forced to submit to a second scan. This all happened in the same dialogue window, I was only intercepted once.
Not really a bug just weird behavior I thought was worth mentioning.