You can safely bet that you'll never hear the full story. The US Navy has been playing tag with other nation's subs and fleets for decades. Not sure why anyone is suprised by this, but of course it sounds better if the media plays it up like this is something suprisingly unusual.
Like the last line in the article where they say they can't find out if a diplomatic protest was filed... Filed with who, over what imagined offense?
One thing that isn't even brought up, is why the sub surfaced or speculation on if he was operating alone. Maybe it surfaced because it had already been "caught" by the escort attack sub? Or maybe it surfaced just to prove the point? Or maybe there was another sub lying in wait elsewhere and the surfaced sub wanted to see what we'd do? Regardless, there is probably a lot more (and also a lot less) to the story than the writer will ever know or even imagine.
Heh... A formal complaint? I can see it now...
The US would like to formally complain that your subs are good enough to sneak up on our most powerful carrier task force. Please stop being so sneaky and scaring us like that. You're being mean, and I'm going home to tell my mommy.

Remember, a japanese fishing boat snuck up on a surfacing US sub just a couple of years ago, and the Russians are still playing bears vs. eagles over the pole.