As part of a previous bug report by me, I mentioned the radio station's core. This is a followup to some of the...consequences...of breaking it. When I took over the radio station, I of course decided to clean house a bit. One of the higher value targets was, of course, a teleporter. The lounge teleporter to the comm array was nicely placed, so I picked up the xenu mainframe teleporter. Went back through the teleporter to the comm array to unload on my ship, that worked fine. Then...went back through the teleporter to the radar station...and somehow ended up somewhere very, very far away on the planet. Didn't check the exact coordinates, but I wouldn't be surprised if it were 0,0. tl;dr: removing the xenu mainframe teleporter seems to make the teleporter from the comm array to the radio station not teleport to its expected destination. could have also been auto-group doing it. wont count that one out.
When removing a teleporter you of course remove the targeting options that were set with it. I am afraid there is (currently!) no way around that. In case a player decides to conquer and overtake a Story POI and later going to that POI for playing the story, the mission will break. :/