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Chipotle Mexican Grill fell short of earnings estimates but met revenue forecasts on Tuesday as sales growth at established restaurants continues slowing down. The company also emphasized that October has been "choppy" so far.

During the third quarter, earnings grew to $4.59 per share from $4.15 a share in the year-earlier period.

A Chipotle restaurant in New York.
Scott Mlyn | CNBC

Revenue increased to $1.22 billion from $1.08 billion a year ago.

Wall Street analysts forecast Chipotle Mexican Grill would deliver earnings per share of $4.62 and revenue of $1.22 billion, according to a Thomson Reuters estimate.

Shares were last 7 percent lower after the bell. (Click here to track the restaurant's stock after the bell.)

Its same-store sales rose 2.6 percent as it lapped a huge 19.8 percent increase last year. This quarter edged above a Consensus Metrix estimate of 2.5 percent. It was mostly driven by an increase in transactions with a 0.7 percent increase from a price hike in steak and barbacoa in some markets.

So far in October, traffic has been "choppy," said CFO John Hartung. The company reiterated this several times during the conference call.

This year, the company has worked to resolve a pork shortage that began in January after it suspended one of its suppliers for not meeting its animal-welfare standards. About 90 percent of its restaurants currently serve its pork carnitas ingredient. It expects to be fully stocked again in pork in by the end of November.

Throughput count fell by one during the crucial peak lunch hour, the company told analysts on the call. It is working to increase this metric, it noted.

Wage pressure has also hit the company. Hourly wages are up nearly 5 percent over last year, Chipotle said. Much of this increase stemmed from "proactive" moves by the company, which explained it is generally not directly affected by increases in the minimum wage.

The company raised its outlook for new restaurant openings to 215 to 225, up from a previous range of 190 to 205.