I don't know a fix, other than playing the mission again, but this is a bug that pops once in a while in this game, always has, even before the GOG-version came out.

It is theoretically possible there was a cloaked ship hidden somewhere, so always wait a while and perform anti-cloak scan and launch probes into space if the game doesn't end when you think you've destroyed everything, but obviously this can only happen when the enemy is Romulan or Klingon, but if that's the case then ships in your fleet should not warp away. Another possibility might be an enemy being "stuck" inside a planet, or having been destroyed/never appeared because it spawned inside a planet and then not getting registered as destroyed. In any case the game did not register that all the space docks were destroyed, the astounding victory is awarded based on how much damage you did versus the damage you received so if your ships didn't have a scratch on it but you destroyed a couple of shipyards and ships, but not all, the game can award you an astounding victory, just like it can award you a victory when you don't destroy all freighters in a convoy you attack.

Thank you for that, great explanation and nice to know I'm not going crazy