I've run into this bug several times. Most recently i was making a constructor. I placed all my gizmo's on it, a construction module, and 2 hyperdrives, but forgot to add a support module. So i noticed i had 4 units left, and support was 5. But when i added it on, low and behold it worked, and i had a constructor with 61/60 space. However, once you save the design it becomes unavailable b/c of the space conflict. You can never access it again. I had to edit the config files to save my intricate design in a new game.