Craig Grannell solving a problem that I used to face daily with the Mac App Store:
>Then it struck me: I have a back-up hard-drive attached to the Mac, which is a clone taken by SuperDuper!, and, sure enough, the Mac App Store seemingly cannot tell the difference between the active volume and the back-up—at least in this case. And so if the Mac App Store tells you that you can’t install an app and you’re using cloning software, try temporarily unmounting the clone and see if that helps.

As Craig’s reader comments, this will also happen if any volume connected to the Mac has this application on it, whether or not it is properly placed in an ‘Applications’ folder. I constantly had this problem with Lion and Snow Leopard being on my machine in two different partitions. The solution I came up with is copying the app file manually so that it is on both — once that is done it works with no problems, odd.