On page 26 of Make: The Ultimate Guide to 3D Printing there is a screen shot of Tinkercad showing the union of a sphere and cube, the 2 possible differences between the sphere and cube and finally the intersection of the objects which creates a dice shape.
When I try and recreate this example in Tinkercad, the differences looks fine but when I try to recreate the final shape, I get a thin layer of the cube or a thin layer of the sphere on a few faces of the object. I have taken care to align the object at each step.