The New York City Department of Consumer Affairs said Monday that Whole Foods Market Inc. (NASDAQ: WFM) had agreed to pay $500,000 to settle allegations that its stores in New York City had overcharged customers for prepackaged foods. The settlement also requires the upscale supermarket chain to adopt certain policies, such as quarterly audits and training of employees about accurate pricing and labeling.

Whole Foods said in a statement that such audits and some of the policies already had been put in place and pointed out that the agency’s investigation failed to find evidence of “systematic or intentional misconduct.”

Shares dropped a bit in after-hours trading Monday but were quiet in the early premarket on Tuesday. Perhaps the company and investors will be glad to have this one headline issue behind Whole Foods so it can look forward to the new year. Shares have been dropping over much the past year, but recently look like they may have found a bottom during the holiday shopping period.

The specialty retailer posted disappointing results for its most recent quarter, due in part to meager same-store sales and a restructuring charge. Investors may have liked the dividend hike and the new $1 billion stock buyback program, though. But analysts were not impressed, as they responded with plenty of price target cuts.

Shares of grocery store competitor Kroger Co. (NYSE: KR) have been on the rise for the past year, up more than 30% in the past 52 weeks. Big-box competitors Wal-Mart Stores Inc. (NYSE: WMT), Costco Wholesale Corp. (NASDAQ: COST) and Target Corp. (NYSE: TGT) have not fared quite as well, but they still have outperformed Whole Foods.

Whole Foods shares closed at $34.24 on Monday, in a 52-week range of $28.73 to $57.57. Analysts have a consensus price target of just $30.31, indicating that they see no upside at this time. Perhaps a better current quarter will lift their spirits — and their price targets.

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