There is a bug that allows one-per-race buildings to be built more than once. No one has been able to consistently get it to happen and to provide a save that allows it to be tracked by the devs. Many players, including me, have thought it has something to do with a race loosing a planet with the building on it. I have been seeing indications that it can happen if a race decides to destroy the building for some reason. The bug then allows all races that have built one to build another one.
How to find it
Download a save here. It is a new game with all expansion packs and DLC and without mods. I saved at turn 100 to see which races have built the Import-Export Center (IEC), which is a one-per-race building. Some had not built it. Those that had built it had built only one and could not build another. The races that had built it are:
Arcean Empire on Baal2. This is the race I'm playing.
Snathi Revenge on Snathi Prime.
Free Trandals on Delta Gladius I.
Yor Singularity on Iconia.
Check all the races that have already built it and see that it doesn't appear in the list of things that can be built.
For the devs, I am assuming that you can do things I cannot do to change things in the game. Maybe you can destroy buildings without having to destroy a whole planet. I will report what I did. I have cheats enabled. In the console I used the god command to be able to look at the other planets. In the galaxy view I looked at planets to find those with an IEC. I can't destroy anything on the planets, so I went back to the galaxy view and selected a planet In this case it was Snathi Prime. In the console I used the destroy command to destroy the planet, so the IEC was destroyed also. In the galaxy view I went to the races, including the Arcean, that had already built one and saw that it now appears in the list of things that can be built. The bug had acted and allowed this to happen.
I then decided to check out some other one-per-race buildings, namely the Computer Core and Central Bank. I had already built these. I reloaded the save to get a fresh start. The Free Trandals planet Delta Gladius I had both of them and and IEC, so I destroyed it. All three then appeared in the list of things I could build. The same bug seems to apply to all one-per-race buildings.
I hope this helps finding and fixing it.