The parent object is scaled unevenly and presumably also rotated. The scaling carries over to the children, so if you scaled the parent cube for its own appearance, the child cube will be warped the same way. With multiple levels of scaling/rotation, things get real weird.
You can do a number of things to affect the shape of the parent cube while keeping its scale at 1,1,1. You can make the “parent cube”'s actual cube mesh a part of a child object, for example; keep the parent’s scale at 1,1,1 and just scale the child. You could also install a plugin like ProBuilder and make the parent cube a mesh in the actual size you want it without needing to scale the transform.