In PI System Explorer → File → Database → Edit Security, the "Permissions for" box always lists all permissions that can possibly be set within PI AF, regardless of the selected objects. Instead, only permissions that apply to the selected objects should be displayed. For example, it doesn't make sense to configure Subscribe, Subscribe Others, Execute, or Annotate permissions for a mapping, so these permissions should not be displayed in the "Permissions for" box. It should also not be possible to configure such permissions in any way (using PI System Explorer, using PI Builder, etc.).
In the event that a permission applies to some but not all selected objects, the permission should be displayed in the "Permission for" box, but the permission configuration should only be saved to the objects where the permission makes sense.