Are ya trying to program an LTR network or EDACS? I'm not sure about EDACS, but I know LTR doesn't use a dedicated control channel. Each frequency just transmits a short data burst every 10 seconds.
You have not stated where you are seeing this. Dmr or P25? If Dmr, do you have the correct lcn values entered in for each freq? P25 gets the info over the air on the control channel stream.
It can't be fixed as the channel frequency itself does not transmit its own LCN info. The control channel data sends the LCN number of a voice channel when it informs where a TG conversation are taking place and also the LCN's of neighboring sites control channels but it doesn't inform of the frequency so you will have to figure out the bandplan, perhaps by using LCN finder.