Really weird thing happened to me today. It's probably a bug, but I've yet to reproduce it again so there's that.
Accepting a mission that requires clandestine delivery when you already have the materials needed for delivery AND entered transponder off messes with your transponder status to stations.
I docked transponder off at Barad B and saw a 10-unit drug mission for Barad B, which I immediately took. When I talked to the dude that accepts the delivery, he stated that I must be hidden from authorities and some such, which I already was, since I initially docked transponder off. So I exited the station, immediately re-docked, and made the delivery. When I came to Jangala with transponder on, I was refused to dock because I "didn't have my transponder on and that there's a patrol tracking my movements." But I had my transponder on all the time, and no patrol actually came to me. Reloading the save seemed to have fixed the issue, but I couldn't replicate the conditions actually needed to recreate said incident.