Interesting. So the Navy did pay attention to Millenium Challenge, or at least to the Iranians paying attention to it...
For those not current on it: Millenium Challenge was a Pentagon wargame played in 2000, brought to the world's attention by the War Nerd and Malcolm Gladwell, in which the OPFOR general, playing (approximately) Iran, sank a US carrier fleet by swarming it with small speedboats armed with anti-shipping missiles (among other acts that were, similarly, equal parts "brilliant military innovation" and "indefensible munchkin-ing"). The Iranian Navy took note of this, and started fielding speedboats armed with anti-shipping missiles for real; these boats are evidently the US's response to that.
Iranian patrol boats always had anti-shipping missiles. They don't have many patrol boats, though, and they don't have many missiles. Beyond that, if you're going to use a missile there's no point in putting it on a boat if your target is in the Straight of Hormuz. You just launch it from land.
The concern is the Iranians (or whoever) would use speedboats packed with explosives and ram them into US ships. Speedboats and explosives are cheap, so this is a pretty easy attack to put together, and if it's a sneak attack you could get closer by having them pretend to be ordinary civilian traffic.
But the attack is pretty easy to counter, too - the Navy issued .50 cal machine guns with a mount that clips on the rails. The M-2 has a range of almost two kilometers and will turn a speedboat into kindling in just a few seconds.
Beyond that, people (particularly Dolan, who thinks everybody not him is an idiot) who point to that particular exercise have a fundamental misunderstanding of the way these things work. You can't get that many people and ships together doing whatever they want and not have casualties. The Navy did stop the exercise, and while they're not talking the most likely reason is the red team wasn't following the rules. The point of these kind of exercises isn't to develop new and innovative tactics - the point is to make sure everybody does what they're supposed to do.
The US Navy already had the ability to deal with swarms by using cluster bombs[1] dropped by airplane. Since the Millennium Challenge, the Navy's CIWS (Close-In Weapons System) has been upgraded to deal with small vessels[2].
The real lesson is that the US responds poorly to violence. Avoiding direct violence has worked well for Iran for nearly 20 years.
This is all fine and dandy, until the software is hacked and the swarming boats turn on the ship they were protecting. I don't trust the US military with making such a technology.
For those not current on it: Millenium Challenge was a Pentagon wargame played in 2000, brought to the world's attention by the War Nerd and Malcolm Gladwell, in which the OPFOR general, playing (approximately) Iran, sank a US carrier fleet by swarming it with small speedboats armed with anti-shipping missiles (among other acts that were, similarly, equal parts "brilliant military innovation" and "indefensible munchkin-ing"). The Iranian Navy took note of this, and started fielding speedboats armed with anti-shipping missiles for real; these boats are evidently the US's response to that.