A picture is worth a thousand words.
I have a shortcut (not sure what the official word for this is) to my Applications folder in my Dock.
When opening it, I see multiple copies of the icon "Xcode.app".
If I "open in finder", I only see one. If I open the launchpad I also only see one.
Don't mind the folder called "Xcode 5", I added this only yesterday while this multi-icon bug has been there for over a month....
Running OSX 10.10.1
UPDATE: The official name for those shortcuts are "Stacks" (http://support.apple.com/en-il/HT201955)