Ok so as the question implies, why does unity do this?
Why doesn’t it just rewrite the folder and the contents in it? Does anyone else have this issue?
1.Delete all the folders you have made by hand. (empty your build folder)
2.Select “Build” once (from the build settings window) and type in your game name.
3.After that just click “build and run” only
Now it launches the game using just that one folder.
It doesn’t. 
As mentioned, “build and run” overwrites it, and if you do just “build”, you can also choose to overwrite the original folder (you get a dialog asking if you want to replace it).
–Eric
Odd, mine just says folder exists but doesn’t prompt me, but that is Unity 2.5.1 on Windows. On the mac it prompts for overwrite. shrugs
Hmm, didn’t consider there would be differences between versions…in that case, I amend my response to “It doesn’t, at least not on the Mac. :)”
–Eric
on windows “build” does not prompt to overwrite thus people using windows that only use “build” to test their game make like a zillion folders.
Thanks guys!
Well I am using Unity on Windows so yeah it doesn’t prompt me to overwrite. Instead it creates a new floder as I stated.
Even if I tried to overwrite it, it doesn’t. But now I know my way around that so that I don’t go creating a lot of copies. Thanks again guys!