Speculating here, so it ain't gospel - and bear in mind that while I HAVE worked closely with US forces, I don't know all the traditions of your branches (you guys have some REALLY nice traditions), or the intricacies of the US - UCMJ.
Who - orders like that come from high up, and are given directly, face to face. Anyone can ask for orders to be given in writing - it's a pretty standard CYA move, but the higher up the orders come from, the less likely that is to happen. A Captain would ask his Commodore (or your equivalent) to put any dodgy sounding orders in writing. He would be highly unlikely to ask a full Admiral for the same. There is covering yourself and there is shooting yourself repeatedly in the crotch to make a point.
What - At a wild guess, travel with weapons secured for storms and not to pull the Sim cards when intercepted. To fake mechanical trouble at a specific point. Only the captains of the two vessels to know the actual orders (that one is pretty standard anyway).
Where - Mechanical "failure" to happen in a highly visible area for opposition patrols. Note they were picked up quickly despite maintaining radio silence.
When - depends on the purpose of the op. If it's to drop in bad intel, it was probably in the works for months. Political feels, could be a spur of the moment thing.
How - see where. Most modern boats are highly automated. It's easy enough for someone with the knowledge and access to pop a nice little time bomb in the control systems.
Why - God knows, and he ain't telling. I'm inclining towards treasonous reasons, but that could be my paranoia about the current crowd.
