The shell itself is made from broadened and flattened ribs, fused to parts of the turtle's backbone (so that unlike in cartoons, you couldn't pull a turtle out of its shell). The shoulder blades sit underneath this bony case, effectively lying within the turtle's ribcage. In all other back-boned animals, whose shoulder blades sit outside their ribs (think of your own back for a start). The turtle's torso muscles are even more bizarrely arranged.
Ed Yong looks at turtle anatomy and how this weird configuration evolved from the basic vertebrate plan. Link