This problem has been mentioned in the 3.1 thread.
I do have ithis issue rather often, but it seems to affect not always the same stuff in every playthrough.
It happened for me so far with: Computer Core, Import Export Center, Central Bank for sure and maybe others as well.
In my recent game I also have two ships equipped with a Plasma Arc P which is labeled a "one per player" weapon.
I do have mods activated, but reduced modded files steadily since I thought they might be to blame - now I only got modded starnames, and two modded event files, so nothing with improvements or weapons.
Another thing I'm wondering - when I changed from vanilla to playing Crusade, I just copied the custom factions made with vanilla into the mydoc folders for Crusade, since I didn't want to redo them all - could this be problematic here? They were all exclusively generated using the in-game editor though, so without any further modding outside what the game offers.
I've changed them a bit in Crusade now and overall they seem to work fine though, so not sure if this has anything to do with it.