How to remove duplicate icons from Launchpad?
This helped me. Try to move the Xcode App to Trash and put it back.
https://stackoverflow.com/questions/12519772/two-xcode-app-icons-in-launchpad-after-4-5-install
What @ruddfawcett said has worked for me. Click and hold an application icon and many applications on that screen will start to shake and they will have a small x appear on the top left of the shaking icons. The apps with the x can be removed by clicking on the x. Don't forget to empty trash once you are positive you have discarded the right app.