When I try to save a ship with unused module slots (which I do far more often then I should), once I hit the save button the modules are shifted around. It appears that it’s trying to fill the ship up from the front to the rear, with a few exceptions. It ends up moving my weapons away from the hexagonal weapon ports, which is killing me. I end up having to fill up all of the free spots with minimal armor to keep the weapons in place, which really heightens the cost of my ships. Otherwise, great game.
This will be fixed in the upcoming 102 patch