I had the problem of an update symbol still remaining on the App Store Dock icon, even after the update had been installed. This was with Coda 2 (ver. 2.02 update).
The symbol disappeared after I did the following:
1) Applied the update through the App Store
2) Quit the App Store
3) Right Clicked the App Store Dock Icon and selected the name of the software requiring the update.
The App Store page for the software was then shown and the update symbol was gone!
I hope this helps.