Oh, I think I see it - don't use Ngons as you have on the docking port disc and the flat surface it's sitting on.
To remove them, select all faces, press F -> clear Ngons. When dealing with geometry destined for FS, stick to triangles and quads only if you have to.
In fact, make the little docking port disc separate from the box geometry, but still part of the same mesh. (Ie, if you select any face on the box and press Ctrl+L to select linked faces, the docking port won't get selected.
Also, your front and back turrets have their normals inverted - select all faces and press W->flip normals to fix.