If it happened the way it was described in the article, then it was probably a probing action in which they come close enough to test our response and then back off. It's a common naval practice --- we used to do it to the Russians during the cold war and vice versa. From a different article I read, the US commanders were in the process of giving the orders to fire, but then the boats backed away.

One thing about "international waters," the Straits of Hormuz are only 12 miles wide, so the channel of international waters is extremely narrow. It is possible to make a mistake by one side or another. With hostile navies in such a small place, this kind of thing should be expected.

The other possibility is that the event did not take place exactly like it was described. I think Bush really is looking for a pretext to attack Iran. So it wouldnt be surpirising to me if the US ships "probed" Iranian waters or otherwise provoked them. When leaders on both sides are a bit crazy, it's hard to say what might have really happened.