Submitted through ZenDesk, but I wanted to put it here too to see if anyone else has seen this before.
Flew yesterday on a route around Alaska, made up a fake Frontier route and flight number. Now, every flight uses that callsign and number in place of an aircraft registration number if I leave the callsign and flight blank. Kinda funny taking off in Cessna 152 as Frontier flight 5244 from a dirt strip.
Zendesk ticket: 119922
Yes, I’m having the same problem.
There’s a trick that you should be able to press the “clear” button on the customise screen. simply deleting the number doesn’t seem to do it, so but there should be a clear button visible somewhere in the bottom to truly clear the flight number.
Either that, or you directly apply the flight number and callsign into the livery aircraft.cfg
That seemed to work. I entered gibberish into the callsign and flight boxes, then tapped my delete key (the clear button disappeared whenever I’d move the cursor out of the box…). Voila, no more ghost callsigns.
Still, definitely a bug. Honestly, I don’t see how stuff like this gets out in a final product, let alone one still there a year after release. While it’s hardly a sim breaking bug, it is something pretty obvious that should have been caught by the devs in pre-release testing. The QC going into MSFS is not the standard I’d expect out of a $90+ piece of software. 
The customize screen should show what all your callsign settings are, like it used to, instead of being blank when you open it.
I also have this issue. Would upvote but under the new trust levels I can’t yet
Same here. Buggy since the last update, I think.