I had the same problem on my first trial on this mission. I dont know what I hit either, but I do recall coming awfully close to a buoy. It caused something like 70% damage. On the second trial, I tried to elimanate any cross track error, which successfully stayed away from the buoys and other ships. In fact, as soon as I hit the first waypoint, I turned to the next and let the ship go full speed ahead without having to check on it or update anything.