the problem is that the SSD is in the same layer as the other capitals. Try clearing a way for the SSD by getting away by nearby capitals.
If it doesn't go where you want it still the enemy capitals and space obstacles cause the same problem too.(asteroids and nebulas).
Let it get around them, you can't do a thing unless you want to go trough. then click within the asteroid field. when the ship is well in, you can click anywhere, it will go straight trough