I just noticed that something like this happened in one of my games - a fighter belonging to the Terrans, who were eliminated long ago by culture-flipping, is still on the map and remains under their control. I can click on it and bring up the details screen, so it seems to actually exist (unlike the "ghost ship" bug that occasionally appears in the bottom of the map).

Try attacking the "Altarian" battleship (save first). I might in my game; since I'm playing with a mod that made the Terrans Super Organizers, it will be interesting to see what happens as a result.

I leave surrenders on for the same reason I always play with mega events: they add an element of randomness.

Anyway, in both my case and the OP's the bug occurred when a race was eliminated by culture-flipping, not by surrendering.

Strangely enough I also received a report that my spies had increased their level of knowledge on the Alterians after that civilization had disappeared.

That's the "archaeologists" LTjim mentioned. It's a known problem and I think affects civilizations eliminated in other ways as well.

The "archaeologist" name for those lost spies was coined by Loupdinour, who made a detailed study of espionage in thread #316263.

He coined the term in reply #3 to the thread entitled "A Q about espionage and"  The thread is #357873.

As he had noted that, if you lose your passive spies when an empire is destroyed when your intel level was below "Advanced", you will still get the normal reports as your intel advances on the dead race.