If you have installed Applications through the Mac App Store, but updates for these Applications aren’t showing as they should, your Spotlight index data may be messed up.

The quick fix for this is to open the Spotlight system preference pane, add the /Applications folder to the Privacy tab, close the Spotlight system preference pane, reopen it, then remove the /Applications folder. This will force Spotlight to re-index the /Applications folder, which will allow the Mac App Store to find your installed software and display updates properly.