Once the CSD is assembled, it may replicate uncontrollably so that it does not stop until it has reduced to nothing but a zillion copies of itself. This will result in a vast seething mass of what is known as "gray-goo" shown below.
Also, if nanotechnology is not correctly applied to the programming of the nanomachines, chaos would occur because trillions of nanomachines would be trying to do their own individual task instead of working together.