The Department of Consumer Affairs conducted a sweep of 700 supermarkets and found that one of out of every two stores failed inspection, for a compliance rate of 48% (violations include "inaccurate check-out scanners, lack of prices on individual items, taxation of items that are not taxable, improperly weighed food, and unavailability of scales for customers"). And in the poorest communities (all in the Bronx), the compliance rate was only 36%.

The DCA says supermarkets have the second lowest compliance rate of all the industries it checks; interestingly enough, bodegas, which are a separate industry, actually have the second highest compliance —82% Citywide and 94% in the five poorest neighborhoods. DCA Commissioner Jonathan Mintz said, “It is a supermarket’s responsibility to ensure that its products are accurately priced and its customers are correctly charged, but with half the supermarkets in the City receiving violations, it is clear that they are failing their customers. We’ve conducted extensive education, met repeatedly with representatives of the supermarket industry, and issued hundreds of thousands of dollars in violations and there has been no improvement. Because thousands of New Yorkers continue to be overcharged, I’ve directed our inspectors to double the number of inspections in the coming year."

You can read more about what your "rights at the register" are here (there should be a unit price indicated; not all foods need a stamp/tag) and you can complain about overcharging here.