Whole Foods has implemented a new inventory management system across all its stores, aimed at cutting waste and making stores operate more efficiently. But employees are complaining that the new system is creating unnecessary problems and causing widespread shortages of food on its shelves.

The new system, dubbed OTS or “order-to-shelf” has strict rules, which has been the source of problems for many store employees, from managers to supervisors to cashiers. According to Business Insider who broke the story, it’s not unusual to see a Whole Foods employee crying due to stress. Some employees who have worked with the company for over twenty years are leaving it behind as employee morale is at an all-time low.

Amazon purchased Whole Foods last summer, and since, there’s been much speculation about plans for the high-end grocery chain, including launching a Whole Foods meal kit service. The new inventory system however wasn’t initiated by Amazon executives.

Whole Foods has typically managed its inventory regionally, with differences in protocol from store to store, which the company argued has led to widespread inefficiencies. The new system relies on paperwork in the form of “scorecards,” which evaluate every part of the process, from accuracy of signage to recording missing items or “shrink,” from store displays, to back room organization. If anything is in the wrong place or there is excess stock in storage, departments lose points. According to one employee, even if an item is one inch outside its designated spot, points are deducted from their scorecard.

Failing scores include anything below 89.9%, and can result in firings. This has led to increasing frustration among employees, who have also said that supervisors and managers don’t understand some of the processes, making it that much more difficult to achieve success.

Some have said a basic lack of training of the new system has contributed to the problem. Others have said the creator of the OTS system has never worked in a grocery store, and included unnecessary checks and paperwork.

Business Insider spoke with 27 former and current employees on the condition of anonymity, and found that not only are employees terrified of losing their jobs, but the new system has led to shortages of food across stores. Business Insider included photos of empty shelves in various Whole Foods across the country, to demonstrate.

"The fear of chastisement, punishment, and retribution is very real and pervasive," one worker told Business Insider.

Whole Foods executives have defended the new system, saying that the company has reduced waste and inefficiencies and allowed employees to spend more time on the floor engaging with customers.

Whole Foods employees are hopeful that Amazon will alleviate the situation with its logistics capabilities. Some said they hope Amazon executives will visit stores and see the holes on the shelf and be prompted to do something.