To avoid this problem in the future (for those who may use these certificates) present your coupon before ordering. I have the restaurant ok use of the coupon so there are no surprises later.
It seems that your problem was with the restaurant, not restaurant.com, which has very good customer service. They will even let you exchange a certificate if you decide you don't want to use it for any reason. (I am guessing that this may change in the future so if you have unwanted certificates, exchange them now.)
btw you would have been able to see that the coupon had already been used if you had checked your restaurant.com account. Once a certificate is phoned in, it should come off the 'available certificates' list on your account. (Your post is confusing because it said you tried to use 2 certificates. Maybe you can explain that better.)