For one thing, autogenerated software lacks a common language. For any software or web of software to start imposing agenda on a growing portion of the autogenerated mass, it would have to, one by one, crack a language for each system it desires. Its power, the elimination of all code, is also a hinderance in this regard.
There are humans that can do this, link them together and make supersystems. But, because it is an intrinsically open ended problem, with no real refinement data, it is unlikely that an autogenerated system can be designed which could do it on the scale necessary to launch Skynet.