If you mean that they have a small yellow box with a plus on the icon, that indicates that they are shared in other folders in the vault.
Michael has it right. We use shared files to segment off the files we share with our vendors/suppliers who provide machined parts. They use our web client to gain access to the files shared in their folder.
I use a VB.Net add-in to pop up a form to show any user all the locations where any of the shared files are shared.