Not very clear either.

I found it my self in the end, it was on display in the bottom of a locked filing cabinet stuck in a disused lavatory with a sign on the door saying ‘Beware of the Leopard.”

Hardly intuitive.

The Lost Citizen button takes the player to the Summery Screen which in my game has 20+ Citzens on it, there is no lost section on that screen nor any indication what was lost or where it can be found or what should be done about it. On the right there is an "In Transit" section with several NPCs listed. If the player looks very carefully, he will spot under the name of one is the word LOST written in small letters.

Just knowing that is not enough though since the player still is not told what to do about it.

I eventually went to the "Transer" Page, found this Citizen marked LOST on a LONG LONG list of other citizens and assigned him to one of my planets, that fixed the problem. 
None of which was explained at all.

I think your going to have too rethink this feature, or at the very least make the Citizen return to the "Working for the Government" list automatically.

Got the exact same problem, can't figure out how to fix it either.

A better solution is to use the "turn" cheat command. I tested and it allows you to continue to the next turn.

Having the same problem here, used the turn cheat to bypass the lost citizen prompt, but there's still the issue of the unselectable citizen ship just sitting in place taking up a space. The "destroy" command doesn't work without it being selectable, or providing an object ID, so...

Hello E static Intersting issue with the enemy citizen capture.. I see if I can duplicate the glitch and see what works to crack it. 

The bug is still there as I just encountered it. It needs fixing. If nothing else, you should be able to click on it like a ship and select decommission. Now I will probably have to invalidate a 256 turn game by turning on cheats.

@ Rhonin_the_Wizard

"Preventing a stuck turn" by constricting a game feature (hopefully) sounds to me as if it is a temporary fix that will ultimately be replaced by a fix to the actual source of the problem. Is this correct?

"Moving citizen on the map make little sense anyway, when you have agent and diplomat moving instantaneously..."

I totally agree with this.  It takes x number of turns for a Citizen to reach a planet, but it can be recalled directly to your home world in the same turn?  Pick one mechanic or another.  I would definitely prefer the latter one.  Everything involving citizens should be instantaneous. 

I opted in to the 3.01 update. I loaded the save but it still showed the citizen as lost. But I loaded a save from just before destroying the ornery citizen, met him again, and this time he stayed blown up. So that bug has been fixed. Thanks for the help.