This is a general explanation which may not be wholly accurate, but it should give a basic understanding of why you need both frequencies and sites on trunked systems...
A trunked system will (routinely) support many departments, all using a common bank of frequencies. A computer keeps all departments sorted out, separated, where each department does not interfere with the others. These frequencies are used to transmit and receive audible communications and are (in most cases) using various geographical locations (more commonly called “sites”). Think of the numerous cell sites our cell phones need. It’s the same with these trunked systems we listen to on scanners.
it sounds like you ignored all sites in a trunked system. Those frequencies you included now have no sites associated with them, which are necessary for the scanner to track where the systems computer is sending each transmission. It’s all done behind the scene with control channels which direct all units on what to receive and where (which site) to transmit.
