I think it's been reported before, but anyway, here it is again.
That bug used to be present in the beginning of the game, got patched, and has sort of comeback.
In my save game below, I have shown how I have 2 deep core mine improvement and in the process of building a 3rd.
At the very least, I should not be able to rebuild these kind of player unique improvement. Ideally, they should be destroyed upon inheriting/conquering the planet, but it might be too hard to code. I'd settle for the first one 
To reproduce:
- build a unique civilization improvement (I don't think it works with "galaxy unique")
- either conquer a planet that contains the same improvement or inherit one through surrender
- build the same improvement again on another of your colonies
- Since the improvement can not be built once more after that, I suspect it's as if the "counter" is reset after conquest/transfer of ownership.
- I can't remember from my previous game if it can be repeated after another conquest or surrender, but I know for sure the improvement stays there, even if it's been built on 30 planets before.
- It is also unclear what happens if I destroy the improvement, if I can build it again or not. I'll let you try on your end since re-loading a save game is a long a turn change, meaning, a couple of minutes, at least
Save game
This my Jennifer II colony where I first built the improvement deep core mine:
This is my inherited colony (AI surended to me, but the same would happen if it was a conquest) Akasha III where there already is a deep core mine:
Finally, this is a colony where I can build a new core mine, Crane II:
