I've never heard of that happening, or the airline collecting an extra fare because 'technically' the rules were broken. Ticket rules are applicable at the time a ticket was booked, and/or for any changes made to a ticket. "Standby" is not a change to a ticket, but is rather, just substituting the use of a flight coupon onto a different, equivilant flight.

Of course, the airline is under no obligation to allow you to 'standby', unless that priviledge has been explicitly written into the fare rules of the ticket.