Mr. Gunther met with a group of ranchers in Omaha in October. Angela Jackson-Pridie, a grass-fed cattle expert in Vermillion, S.D., who took notes at the meeting, said he told them that individual Whole Foods stores would buy sides of beef or smaller sections directly from producers. But ranchers said that other executives in the company told them in January that Whole Foods would buy only certain parts of the animals, leaving the ranchers to market the rest themselves. Mr. Gunther did not return calls seeking comment.

Allen Williams, chief operating officer of Tallgrass Beef Company in Kansas, which has been trying to sell Whole Foods its beef, said, “the company backed way off what Gunther said. Within Whole Foods there is a monumental internal struggle to decide how they are going to do business in the protein sector.”

Whole Foods buys its private label milk from Cropp, a cooperative of organic family farmers who receive high marks from the Cornucopia Institute, a nonprofit agricultural policy research group, for humane treatment of organic cows.

But despite continuing criticism that Horizon Organic gives its cows very little access to pasture, Whole Foods continues to sell Horizon’s products.

A spokeswoman for Horizon said the company is in compliance with Agriculture Department standards.

When the public learned that farmed salmon has color added to its feed to make this otherwise grayish fish look like wild salmon, its much pricier cousin, Whole Foods said it would put “color added” on labels for farmed salmon. But visits to many Whole Foods stores over the last four years revealed that “color added” does not always appear on the labels of the farmed salmon, an error probably made at the store level. When employees behind the fish counters at several stores were asked if the farmed salmon had color added they were unable to answer.

In tours of eight Whole Foods stores in the Washington, D.C., area and in New York City and suburbs over the last several months, other problems suggested inattention to detail. One-third of the Yukon Gold potatoes in one display had turned green; some sweet potatoes were shriveled; cherry tomatoes in net bags were wrinkled; net bags of organic lemons contained several that were past their prime; and packaged haricots verts were brown. Six containers of one brand of yogurt available for purchase in the Bethesda, Md., store on Jan. 21 were stamped with a “use by” date of Dec. 28.

On that same day Elise Klein, who considers herself a devoted Whole Foods shopper, was returning shredded cheese, yogurt, cereal and several other items at that store, demanding a refund because all of them were out of date. “You guys need to monitor yourselves better,” she said.