This only happens with one-per-planet improvements that can be upgraded, like Fusion Power Plant. To reproduce this, use the following steps:

-build a Fusion Power Plant
-upgrade it to a Anti-Matter Power Plant
-give the planet to a race that doesn't have the Power Plants in its tech tree (like the Drengin or Yor)
-take the planet back (by invading it, trading for it or the like)
-if you now try to rebuild the Anti Matter Power Plant, you can't, because it is no longer in the list of available buildings

This happens because the upgrade counts as a second building, as far as I can tell. So, when the actual building gets destroyed, the game still thinks there is one. I first noticed this bug in my mod, because I changed a lot of buildings into upgradeable one-per-planet improvements, but could also verify it in the vanilla game.