Catching an illegal move too late in Castles of Burgundy
We frequently play games for the first time and as a result often get the rules wrong. Our solution to this problem, when we realise a rules infraction too late to reasonably unwind it, is to continue the game allowing all players to repeat the error - so we're all playing on a level playing field. 

I.e. in your case continue the game but let other players place two of the same building into an area for the rest of that game.