Why would a grocery store (e.g., Grocery Outlet) refuse to honor a manufacturer's coupon?

The reason Grocery Outlet does not accept manufacturers coupons has to do with the unique buying relationship with the manufactures. Many times manufactures issue coupons to boost sales of overstock or new items or to help sell out prior to a pack change. Grocery Outlet will buy these items at a lower cost than a traditional grocery store would so in essence that coupon has already been built-in to the price the consumer is paying. There will be on occasion be times that Grocery Outlet will do specific item coupons, but they prefer not to play a high/low game with a bunch of tricks. Instead they will have low prices across the board. If there were coupons attached to the individual packages more than likely those products were originally intended for another retailer at a higher retail price.

Grocery stores are free to choose their own coupon acceptance policies.  Accepting coupons does have a labor element to it because the retailer must then sort the coupons and send them to a clearing house (or two) to get reimbursed for the face value of the coupon as well as a small handling fee.  Some chains just don't want to put that sort of effort into it.  Also, some stores will only accept coupons up to a certain limit (for instance many don't accept "Free" coupons because of the potential fraud associated with exceptionally good deals).

It's possible that the cashier was incorrect.  I've had consumers report to my company that coupons we gave them were not accepted at a particular grocery retailer but then we receive hundreds of redeemed coupons back from the exact same retailer.  There were maybe some cashiers at that chain who were confused about the legitimacy of the coupon they were receiving.  Different cashier, different policy.  Maybe?