While it's recommended you store asparagus in water to keep it fresh, Whole Foods decided to place a few spears in water bottles and sell it for $5.99.

The price of this "asparagus water" was shocking at the time. Making matters worse was that they sold entire bunches of fresh asparagus for $5, a far cheaper alternative.

Whole Foods customers brought the company to court over its 365 Fat-Free Plain Greek Yogurt, which used far more sugar than was printed on the label.

The label stated it had 2 grams of sugar for every 8-ounce serving. However, Consumer Reports conducted its own test and discovered it contained 11 grams of sugar per cup.

In 2015, the New York City Department of Consumer Affairs discovered Whole Foods' "systematic overcharging for pre-packaged foods."

Findings revealed more than 80 packages with incorrect weights, with 89% of pre-packaged items exceeding the legal margin of error for misclassified weights.

Whole Foods set up a grading system for its organic-certified produce in 2014. However, it required farmers to pay thousands for tracking systems and paperwork.

Experienced certified organic farmers also became upset when nonorganic produce received higher marks and were given the "responsibly grown" designations.

In addition to produce grading, Whole Foods also introduced a compliance scoring system called Order-To-Shelf for its employees to reduce waste.

The system required tracking everything in the store, but longtime employees claimed the benefit wasn't worth the stress. Staffers reported layoffs and firings across the board.