I had this same issue as well.
I ended up calling Apple Support about the issue. After being on the phone for an hour and trying every thing to fix it, we determined that a certificate was messed up and the server had to be set up from scratch again. I had to reinstall the OS on the Mac Mini Server then reinstall the server app. After setting things back up again everything for user VPP enrollment and pushing apps works now.
My server was still in the testing stage so it wasn't a big deal for me to do.
Did you try removing the user from the program under the user account's About tab in profile manager? Or does the user not show that they're actually enrolled? (Mine wasn't showing they were enrolled but gave that error message you stated)
There is a way to remove Profile Manager content from the server using a Terminal command, i'd try to do that before completely re-doing the server.