The problem is, I think, that someone, something, somewhere, did detect the Crystal, but didn't act on it. The technology almost certainly worked right. It was likely the people that screwed everything up. The Crystal was probably on autopilot with no one (awake?) in the bridge and it would appear that the Fitzgerald was in the same state.

That said, for the US this is a pretty serious embarrassment, because it screams "not combat ready".