http://techforums.nintendo.com/thread/36211?tstart=0
It appears that there might have been a slight delay before the Bayonetta bundled price appeared, but if you give a call to Nintendo's 1-800-255-3700 (6 am ~ 7 pm Pacific, everyday) Customer Service number, or use their webform to contact them, one of the service representatives should be able to refund the difference.