Sometimes when I'm in build mode, I click to build a "one per city" building, and the game doesn't unselect the building I just built; in fact, it allows me to go ahead and build a second one. So I can, e.g., get two Irrigation improvements in my farming city -- nice! But probably not what you intended. This one goes back to beta, actually, but since it's not fixed I thought I should report it in case it had gotten lost in the shuffle.
I wonder if it could be some sort of race condition between the code that updates the number of buildings in the settlement and the code that checks whether you're still allowed to build the improvement you just put down?