When was the last time you updated the game?
The game was afflicted by a bug where systems didn't get correctly updated during turn processing, so multiple instances of a building could be built when there already was one. But a recent update *should* have fixed this. So either Mike has accidentally reintroduced the bug, the bug was never actually fixed, or you haven't updated your game recently.
If on the other hand your were referring to multiple buildings being built in the same turn, the game is programmed to do this. For instance, if a building only needed 5 more industrial points to complete but you were producing 100 industry, the remaining 95 industrial points would then be put into the next building in the list. If the second building is also completed, the remaining industry would be put into the third, and so on. This is one of the improvements in the game over BOTF.
,its one thing that all 4X games (or any with lots of building, really) should have!