First, management deficiences. At that time the purges of the late 30's created lack of qualified managers.
Second, the state of railway network and rolling stock. Also the logistics from railway to army location seem to be hindered by road quality and transport availability (the mass truck, Polutorka, was relatively small and not available in enough quantities.
Third, the quick advances of Wehrmacht disrupted the flow of raw materials and parts between the factories, thus further limiting production. also, since the autumn of '41 many factories were being evacuated, effectively shutting down.