I picked up a Brotherhood distress beacon that was part of a mission. It went to my Junk pile. I dumped it on the ground in my town to scrap it and break it down into base resources. Now when I go to my town I pick up a distress beacon on my radio that leads me back to the place where I scrap items. Basically it seems that the game creates whatever object manages the homing signal when the beacons are dropped on the ground, but doesn't delete it when the beacon is scrapped.