I had the same issue.
The Problem was that i had files and folders in my Windows Project directory which were not listed in my UE4 project directory.
It seems that sometimes when you delete or move a file or folder in UE4 Editor it does not delete or move it in the Windows Explorer.
So to fix your packaging error go in your Windows Explorer and make sure the file and folder tree of it is the same you have in UE4 Editor.