The same thing has happened to me
twice when fighting the Primordius Fortress -- the Fortress is gone, but the game won't end the battle.
The first time it happened, I had to exit the game as you did; but the
second time, I figured out what was causing it because I happened to have the Torc…
The Primordius Fortress dumps out Necrodrone fighters that can CLOAK, yes? Well, when I looked very
very closely, and then moved my ships around to verify what I thought I was seeing, I noticed that there was a single cloaked (and therefore semi-transparent) Necrodrone sitting on top of one of my ships, following it around as it moved.
[Incidentally, this would have been a perfect occasion to have the "magnifying lens" that SAIS had.]
I couldn't get the "hover-over-it" ship display for that Necrodrone -- because, of course, it was cloaked -- but I assume that its weapon had been destroyed in the earlier fighting, and that's why it wasn't UN-cloaking to attack; and because it hadn't retreated (for whatever reason), there was still an enemy left on the screen.
So the battle wasn't
really over yet.
But one quick "FIRE" command later, it
was. 
If I hadn't had the Torc, the Necrodrone would have been
completely invisible; but I imagine it wouldn't have been too hard to get the little bugger anyway, especially with the PVC or an area effect weapon like the Micrometeorite Gun.
The next time that happens to you, get all your ships close together so the screen will zoom in as far as possible. Then if you have the Torc, just look for the cloaked Necrodrone and manually target the spot where it is. If you
don't have the Torc, then just have your ships start firing at each other until you hit the Necrodrone by chance.