I'm not sure if this is a bug with Piratez or just xcom in general but I had a Courier ship performing a courier mission in the pacific region, and after following it for a while it 'landed' in the middle of the ocean and the map used for the fight was the surface of Mars map. The geoscape picture is as soon as the game returned to geoscape so where the ship is, is where the ship 'landed'.
I think this happened before, a freighter I was following also landed in the middle of the pacific, but I was following with an interceptor instead of a transport and so I declined to attack and the ship just immediately took off again.