Occasionally I've had luck logging in as the user and looking at their notifications that way. Usually I just tell them to forward me the email notification so I can take a look.
The two places I've seen alerts cause confusion are the 'Issue Added to a Project I'm On' which can trigger unintentionally when someone winds up added to an active request queue, and similarly if the People tab in a new template isn't cleaned up then sometimes wayward alerts go to people that aren't involved with it at all.
