In the Beta 4B post Brad made he noted that freighters from defunct or problem routes should retask after a turn. It's not working that way for me. The freighter show up near a planet and takes focus briefly each turn but the player can't do anything about retasking it.
It's happened multiple times where multiple freighters throughout the course of the game will just sit there for many, many turns.
You can destroy it if you select it though.