Named cals are user specific. So the admin must have assigned these users a named cal. So they are not unused. if you go in Setup --> Licences --> QVserver --> Assigned cals you should be able to verify that.
So it is not uncommon that they used both, if the used two different ways to open an application : IE plugin and Ajax for example.
Has "Allow dynamic CAL assignment" been enabled in your QVS? See QMC->System->Licenses->QlikView Server->Client Access Licenses (CALs)->General, and the corresponding tab for Document CALs attached to your document.
BTW which version of QVS are you running (please be specific, there are quirte a few different releases of QV 11.xx)?