Macworld points out that Apple has added a new drop-down dialog box to the Mac App Store (above). It alerts customers who are about to purchase an app they've already got installed. While it doesn't fix an ongoing issue, it's at least a nice heads-up.
Software is being added to the Mac App Store all the time. Many are new titles while several have existed long before the store did. Today, customers who bought apps before the store debuted are faced with a dilemma: update that software manually or enjoy the benefits of the Mac App Store -- like simple updating and easy multi-Mac install