The FDA fired off a warning letter to Whole Foods co-CEOs John Mackey and Walter Robb earlier this month concerning what the agency called “serious violations” it uncovered while inspecting one of the company’s food preparation facilities in Everett, Massachusetts, in February.
The letter, dated June 8, stated the FDA found various items, including pesto pasta, mushroom quesadillas, egg salad, and couscous, being stored in areas where “condensate” was leaking from ceiling joints, a doorway, and a condenser fan.
An inspector found several other violations, as well, such as failure to sanitize food prep surfaces, dirty dishes near food, a lack of hot water for hand-washing, and an employee who sprayed an ammonium-based sanitizer on “an open colander of salad leafy greens.” 
Having hot water might not have made much of a difference because, additionally, the FDA said Whole Foods employees did not wash hands between tasks, nor did they wear gloves. 
Investigators didn’t find evidence that the Whole Foods facility harbored any pathenogenic bacteria – 1 out of 100 swabs taken on surfaces that come into contact with good and other surfaces tested positive for nonpathogenic listeria. But based on the agency’s findings, the perfect conditions exist for bugs to spread.
Based on this finding, the FDA said in the letter that “conditions exist in and on your equipment that would support the presence and growth of Listeria monocytogenes and indicates that your cleaning and sanitation practices may be inadequate.”
“Your response includes retraining of employees as a corrective action for most of the observed violations but you failed to mention adequate supervision over your specialized food processing operations and how retraining will ensure sustained compliance. We do not consider your response acceptable because you failed to provide documentation for our review, which demonstrates that all your noted corrective actions have been effectively implemented.” 
Whole Foods was given 15 days to respond to the FDA after receiving the warning letter.
The company has faced problems in the past, including complaints that it charged customer exorbitant prices for somewhat silly items, earning it the moniker “Whole Paycheck.” Some consumers also freaked out after discovering Whole Foods sold peeled oranges in plastic containers, saying the practice violated the company’s own eco-friendly policies.
But Whole Foods is engaged in a lot of good stuff, too, such as making plans to power some of it stores with solar energy, and committing to GMO transparency.
 CNN Money