Creo que tu UPDATE la sintaxis es incorrecta. A ver si esto funciona:
UPDATE booked r
INNER JOIN (
SELECT a.st_code as from_t
, b.st_code as to_t
FROM `stops_at` a
CROSS JOIN `stops_at` b
WHERE (a.stop_no < b.stop_no)
and (a.train_no = b.train_no)
and (a.train_no = '11280')
) new
ON r.st_from = new.from_t
and r.st_to = new.to_t
and r.date = '2013-04-16'
SET r.seat_ac = r.seat_ac-5
