They come from "kitchen table" chip brokers who get them from China. Then the pentagon/contractors purchase from them because of federal rules encouraging "cheap and disadvantaged" suppliers ie people in their basements ordering their "stock" from ebay. Controls are already in place to ensure tracking of components from the factory through the distribution chain to the end user. It's only when companies take shortcuts that counterfeits slip in.
many of this chips are probably made in what is known as a "midnight run." good chance there is no difference between the counterfeits and the originals. They are produced at the same facilities in off hours. Sometimes the materials that are used are questionable though.