The 852.6875 MHz alternate control channel for Copper Mountain is the primary control channel for Mesa Point and the 853.500 MHz alternate control channel for Betasso is the primary control channel for Redlands. If you compare the Copper Mountain and Mesa Point sites or the Betasso and Redlands site, you will notice that they almost share the same frequencies by design. The frequencies for sites are commonly reused when there is enough distance or geographic separation (like mountains) where there is no chance of the sites overlapping and interfering with each other.
Scanners are not smart enough to know the difference, so it will show whatever active control channel it is receiving and the site it was programmed under.
I agree with RMason's reply, you probably have too many sites programmed if you imported the entire system and are experiencing duplicate control channels. The scanner will scan for every single site and every control channel programmed unless you have a GPS addon, which means you have a good chance of missing traffic while it is scanning. DTRS has 243 sites in the database with most of them using four control channels, so that more than 900 different control channels programmed for the system that it is checking every scan cycle.