I've got exactly the same problem. Survival Mode, so no save left by the time I figured out something was wrong, I've got a Vertibird stuck circling around where it was originally called. Won't land, can't focus it in VATS or shoot it down, and any attempt to summon a new one will say "The vertibird will be unable to land here". No luck with console, tried kill, disable/enable, resetai, resurrect, no go. Even tried going away, waiting ten days to get the cell to reset, came back and it's still there and I can't get a transport. Anyone got a clue on this?