Who polices the police? Or, more broadly, how does a big bureaucracy keep all its operatives on the same page?
The short answer: they don't, at least not in a nation as big as the U.S. An example, which I ran into while working at USDA, is the US Postal Service (and which I was reminded of while reading the NASCOE negotiation notes). USPS has written directives for its local post offices, but that doesn't necessarily mean that the local postmaster in Podunk, Iowa (why do we pick on Iowa?) has read, understands, and follows it.
When you bring two big bureaucracies together, like USPS and the Farm Service Agency, you reveal discrepancies. If FSA and USPS in DC reach an understanding of what directive A means, FSA tells its field offices to do X, Y, and Z based on that understanding. But when the field office operative reaches the local postmaster, he or she may have a different understanding. Result: confusion and inefficiency.