A number of customers self-reported symptoms such as vomiting, diarrhea and nausea to the website iwaspoisoned.com after eating at a Chipotle on West Pico Boulevard in LA. This website allows patrons to anonymously report incidents in which they believe they have gotten food poisoning at a restaurant.

"Public Health routinely monitors for and investigates reports of foodborne illness and communicable diseases in response to health concerns," the Acute Communicable Disease Control unit of the Los Angeles Department of Public Health, told CNBC via email.

Public health officials in Los Angeles are investigating a possible foodborne illness outbreak at a local Chipotle restaurant. The news was first reported by Business Insider .

Shares of Chipotle Mexican Grill fell more than 3 percent on Wednesday after reports surfaced that the fast-casual chain's food safety woes are still not behind it.

"We take any report of illness very seriously. We are aware of a few reports (two of which appear to be the same) on user generated reporting sites but there is no clinical validation associated with those reports, and we have not been contacted by customers directly to substantiate these claims," Chipotle spokesman Chris Arnold told CNBC via email.

Arnold told CNBC that the company is not aware of any reports made to local health officials, but noted that the Centers for Disease Control and Prevention had reported that influenza was widespread in California.

He also said that several employees that had been ill were "being held out of work," as per Chipotle's sick policy.

"So all of this is happening against a backdrop of widespread illness throughout the state," Arnold said.

Even if Chipotle is not to blame for these incidences, the report once again puts the company's food safety polices under scrutiny.

It has been two years since a string of food safety incidents first battered sales and scared away diners. While the chain has been able to battle back and return to profitability, its successes have been overshadowed by more recent incidents.

A number of reports have surfaced in the last year pointing to a lax sick policy and some food safety procedures that were not being followed. Chipotle has implemented a paid sick-leave policy to ensure employees stay home when they are ill and has held several meetings with its entire staff of restaurant employees to reiterate food preparation practices.