This is not a bug, people are not understanding the wording of the 'rules'.
The re-roll rules state any ship not available in the legion containers. There are just 2 ships listed for the small containers, 3 for the medium and 3 for the huge. The substitution list is just that IT IS NOT THE LIST OF SHIPS IN THE LEGION CONTAINERS. So yes you can get a ship from the list that you already have, and get dbl compensation.