The Coast Guard did run a training exercise in the Potomac on 9/11, very close to where the president was at that particular moment (at the Pentagon). Needless to say, that is likely a decision that will come in for a good deal of second-guessing.
The Coast Guard was running the exercise on their Coast Guard radio frequency. So call outs tied to the exercise -- i.e., 'Okay, we've just fired 10 rounds at the suspicious vessel' -- went out over the radio.
Only the press listens to those frequencies. And they went into scramble mode when they heard a Coast Guard officer talking about firing on a suspicious vessel. And it pretty much all went from there.
CNN's Kyra Philips says that CNN went up with the story as breaking news without confirming what was happening with the Coast Guard. That looks sort of iffy in retrospect. But when you think about it, if reporters hear Coast Guard officials talking on an emergency frequency about firing on a suspicious vessel in the Potomac on the anniversary of 9/11, I think there'd be a pretty decent rationale for sounding the alarm.