I played around a bit and I don't think the line is caused by the little deviation.
When I create similar objects where everyting aligns perfectly, I can still get those "lines".
I think it is caused by anti-aliasing and how the stacking order of the objects influences the calculation of the anti-aliasing.
With Anti-aliased Artwork Checked in the Preferences, lines show in GPU Preview and CPU Preview.
Unchecking Anti-aliased Artwork in the Preferences shows it in GPU Preview, but not in CPU Preview.
Moving the lighter objects below the darker ones hides the lines in both GPU and CPU preview with Anti-aliased Artwork Checked in the Preferences.