In the clearest example yet, the Food and Drug Administration this month sent a stern warning letter to Whole Foods Market, a longtime champion of fresh and healthy foods, saying that the company had failed to address a long list of food safety issues at its food processing plant outside of Boston.

Among the problems cited: condensation dripping from the ceiling near food; an ammonium-based sanitizer used on a work surface near the preparation of a salad; and a failure to separate dirty dishes from ready-to-eat-salads.

The letter from the F.D.A. is just the latest headache to afflict Whole Foods. Over the last couple of years, the company has struggled with slower growth as competitors have gotten better at copying what it did to distinguish itself in the grocery market. Other wounds have been self-inflicted, like last year, when the New York City Department of Consumer Affairs called it out for mispricing some merchandise based on weight.

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