This has been an App Store anomaly for awhile but there is a workaround.
You can delete an app using this free utilty >Download AppCleaner for Mac - Uninstall your apps easily. MacUpdate.com
That deletes the app and all the associated files.
Then re download the app from the App Store. That should install the lastest version avaiable without seeing Updates available.
How to re download apps from the Mac App Store:
Open the App Store. From the menu bar click Store > Sign In
Click Purchases from the top of the App Store window.
Select which apps you want to re download. Then right or control click where you see Installed then click Install.
Make sure and use the same Apple ID used for the original purchase.
You can submit feedback to Apple if you'd like. You're not the only App Store user that has reported this problem.
Apple - Mac OS X - Feedback