It wasn't a Navy missile. It was a missile fired by Iranian mercenaries hired by a wealthy Iranian family to enact revenge for the shooting down of Iran air flight 655, by the USS Vincennes back in 1988.
And I can't tell you how I learned this, and no, i'm not joking.
This makes sense to me. It explains to me why the Navy was on the scene, as if they had information and were expecting something. It explains why the administration didn't want to respond to the attack. It explains why the CIA was involved in cooking up the cover story (that by itself always struck me as very odd in itself). And it explains why they were so determined that it was not terrorism... indeed, they announced what the results of the investigation would be before the investigation started. This makes a kind of sense.