When a user tries to remove a permission from the SSO UI using the minus sign "-" at the end of the permission information the UI initially shows the permission as removed, but if the webpage is refreshed the permission is still there.
The minus sign "-" at the end of the permission information in the UI should be activating the "Update Resource" button to save the change. This is currently a know issue and will be resolved in a coming release.
As a workaround, add a permission, type in it, and it enables the "Update Resource" button. This will allow saving the deletion of the unwanted permission.