I presume you are referring to Shortcuts?
Shortcuts normally have an arrow at the bottom left-corner of the icon.

Are you sure it is a duplicate or is one of them the original file or folder?
Right-clicking each version and choosing Properties will show you the details.
Only Shortcuts will have a listing called Target which will show what the shortcut is pointing to to open.



The only reason I can think of duplicate icons appearing is if you right-click the icon and accidentally choose Duplicate (such as at some point before you reboot or just after you start your computer.) This may happen if your control over the right-click is not smooth.

Program Shortcut . . . . Folder . . . . Folder Shortcut


* Edit: Make sure you periodically check your computer with security software to ensure your computer is not infested with a virus, malware or some other form of nasty code.