For fast-food vets, this is not a surprise. Two for $6 Whoppers does not translate to each single Whopper costing $3. I saw a guy storming out of the Monument Burger King recently because he did not want an even number of the burgers. He was with a friend, and I assume they maybe wanted three total sandwiches for $9. But that's not how it works.
Be sure to watch your mail for weekly BK coupons, too. $6 isn't too bad if you really need to get Whopped that bad, but that's a full day of calories for most people, so you might want something else if you're eating alone or planning on another meal at some point in the day. Sometimes, the deals running in the restaurant are just as tempting as the coupons, so be sure you use the ones that make sense.