"It's just something that went viral in the media and it has hurt our trust and we do feel like we're victims," Whole Foods co-CEO John Mackey said Wednesday during an earnings call.
Whole Foods came under fire last month after a New York City investigation revealed that several stores were mislabeling packaged foods and selling them for more than they were worth.
City inspectors claimed it was the "worst case of overcharging" that they had ever seen, according to the Daily News. Customers threatened to boycott the grocery chain, as a result.
But Mackey said he didn't think the problem of overcharging was specific to Whole Foods.
"We don't think our track record is any different from any other supermarket," he said. "We don't know why Whole Foods was singled out for this attention...We don't know why the media went wild with this."
Mackey and co-CEO Walter Rob published an apology video following media coverage of the investigation.
"Straight up, we made some mistakes and we want to own that," Robb said in the two-minute video apology.
The executives said the overcharges were unintentional and that they mainly occur with packaged fresh foods like sandwiches and juices.
"It's understandable sometimes that mistakes are made," Robb said. "They are inadvertent. They do happen because its a hands-on approach to bringing you fresh food."
Mackey said on the call Wednesday that the company is already taking steps to fix the problem.
"We've done our own auditing, we've put in procedures so we can perhaps be perfect," he said. "If you look at Whole Foods' record these are inadvertent errors."
Executives said last month that Whole Foods is going to retrain employees in New York stores and around the country to address the problem.
The company will also refund customers for the full price of any product that has labeling errors.
"We want to be perfect in this area," Mackey said. "We don't want there to ever be any mistakes."