My daughter worked at a drug store and received coupons helping a "super couponer". They were about $250.00 and now the store says she stole them.

A private business cannot "prosecute" a criminal offense; only the state can do that. For that to happen, the business must file a complaint with the appropriate authorities, who will investigate and determine whether they want to pursue the matter. Whether the authorities pursue it will depend, among other things, on the strength of the evidence, the nature of the alleged wrongdoing and whether the result is likely to have happened through inadvertence or mistake. It is not possible to predict the outcome of such a matter without many more facts.