Originally Posted by
armstwa
.... I called and the rep stated that Whole Foods was not counted as grocery since it sells other things as well....
Welcome to FlyerTalk. It may be that Whole Foods (or some specific location) is not coded as a supermarket, but that would not be the reason. Merchant categories are assigned by the merchant's "acquirer", the entity which processes their card transactions. You can see the category online if you expand a posted transaction to view the details. What does it say?