The same thing happened to me tonight ...
I already knew the crime system was wonky but i was pretty much fine with it (basically avoiding illegal stuff). Problem is, after i spent month raising my fed rank to lt commander through standard gameplay i wanted a little boost so i went to two remote systems 500ly away from my home base (Rhea in this case).
Doing tons of missions, mostly the data delivery and some trading / goods deliveries, i was interdicted and attacked by a clean NPC. Therefore, when i retaliated i got a bounty of like 200Cr (really, close to nothing wich makes things even more ridiculous ...). At some point i was, anyway, 300ly away from the nearest IF (and even then, the map was not showing any at all when filtering and looking here and there).
I used the EDDB and noticed one but, as i said, 300ly away ... I chose to turn myself in, i mean its just 200Cr right ?
Got teleported on foot (yeah i left my ship while walking the concourse just before turning myself in, dumb right ?), 300ly away then, on the prison ship. without my ship of course. Still, i thought, Okay i lost some time for nothing but, nevermind, i'll just go back.
I book a shuttle to Maia (i suspect this is where the original post talked about - the ceos - sothis systems being a really nice place for federation missions). Then on the concourse of the local starport i go to the inter astra counter to get my ship back.
Of course, no one there ... Why should i think otherwise ?
between the various UI bug, the game itself that wont close until i force shut it through task manager AND by closing steam (yes, it is that bad), i've seen the all concourse disappear, showing weird space and graphic glitches, along with parts of the station i was on. The icons in the UI are unbearable, i looked for days and found no guide whatsoever as to what they all actually means. When i switch back to horizons, most of the bug simply vanish and the game closes fine.
I lost hours of gameplay, this is really frustrating. all that because of a ridiculous crime system which basically screams "broken" (makes millions by slaying local factions military ships like a AC:Odyssey misthios = no consequences, but gets jailed hundreds of ly away for 200Cr ?? really ???).
Now i'm scared of disabling odyssey to see if i will get teleported back to my ship (because my last ship is displayed at the game start menu so i guess its still registered as if im in it ...)