Just because a radio ID comes through a site does not mean that that radio is affiliated with that site. It means that someone else has a radio on the same talk group as the first radio and is listening on it.
It would be like having two radios, one in Kansas City and one in St. Louis, each affiliated with a different tower on the same talkgroup (say MO IO 4). When the Kansas City radio transmits on the talk group, anywhere someone is listening to this talk group, their id will show up on the tower showing who is talking to the other radios.
Clear as mud now?