Some minor things I found and took screen shots of.
The first one... you can see the entrance to the ship through the window. Is this supposed to be that way?
http://i1082.photobucket.com/albums/j361/pipboy1981/GhostShip-1.jpg
The console shows a soviergn (in the engineering section of the ship during the mission) but the mission takes place on a miranda class. Not really a problem.. just an annoyance I suppose.
http://i1082.photobucket.com/albums/j361/pipboy1981/starshipconsole.jpg