Ok I had the same issue and its now resolved.
Go to Applications and then click edit (make sure customizable grid is selected) then scroll thruu your applications and go to your phone,.message and contacts logo and drag them to the very bottom beside the home icon.. Then hit menu and then save..
What happened is that your dock icons ended up being mixed in with your applications.
The same thing happened to me, all I had was the application dock icon and the rest was missing. Good luck! :-)