The game compares two cuboids from the given coordinates to judge the overlap. However, the two cuboids do not frame the entire selection area for cloning.

for example：
/clone 0 5 0 1 6 1 1 6 0

As expected, the source area is a cube with 2 meters of side length. And the source area overlaps with the target area. But the game will not judge they overlap.

After many tests, I think that the game judges overlap as shown in images.

Other examples：
/clone ~ ~ ~ ~ ~ ~ ~ ~ ~
/clone 0 5 0 2 7 2 2 7 0