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Turns out there might be a reason Whole Foods is not America's favorite grocery store.

New York City investigators have launched a probe of the chain after finding that local stores have regularly overcharged shoppers over the last five years, according to a report by the Daily News.

The investigation comes just a year after Whole Foods had to pay an $800,000 settlement in California because inspectors found the chain caused customers to overpay for food that was priced by weight.

In New York, consumer protection agents say they found violations that included inaccurate weight labels on pre-packaged food and adding tax to non-taxable items.

"Our inspectors told me it was the worst case of overcharges that they've ever seen," New York City Department of Consumer Affairs Commissioner Julie Menin told the News.

A spokesman told the News the chain never intentionally mispriced items, and other industry representatives have pointed out that mislabeling is often the fault of manufacturers packaging foods—not grocers. And the News also found that mislabeling sometimes actually works in a customer's favor.

One takeaway?

It's a good idea to check food weights using grocery store scales, even on pre-packaged items.

It also pays to compare prices for your favorite foods at different chains: MarketWatch has found that items like hummus can be less expensive at Whole Foods, while many others like produce and cheese are cheapest at competitors like Trader Joe's, Target, and Safeway.

Finally, if you're a Whole Foods die-hard, shop smart; the best sales are apparently on Wednesdays.

Read More: Here’s How to Save Hundreds on Groceries