The ticket "class" won't identify standby - and I bet the agent actually thought you were confirmed. (Just curious what airline this was on.) The "Y" was the fare class, which has nothing to do with whether you hold a confirmed seat on the plane. Some airlines through the CRS systems let the agency sell a seat and issue the ticket and then decide later that the flight was full and waitlist you after the ticket was issued. This generally will not happen with the US carriers anymore due to better interactivity between the systems.