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Why Chipotle's pulled pork is such a problem

Half a year after Chipotle first suspended a key pork supplier for not meeting its animal welfare standards, about 40 percent of its locations still do not carry carnitas, and that's a problem for the chain.

On Tuesday, the restaurant reported comparable restaurant sales growth of 4.3 percent. For many other restaurant chains, this would have been a blockbuster quarter. But at Chipotle, investors have grown accustomed to high figures—helped in part by a price increase last year—and the number missed forecasts.

Partly to blame was the lack of carnitas at a large number of locations.

"We still think we're being hampered by not having carnitas, and we think that could be as much as a couple hundred basis points" off same-store sales growth, said Chipotle CFO Jack Hartung on the company's conference call. To put that in perspective, 200 basis points equals 2 percent.

Customers enter a Chipotle restaurant in New York
Scott Mlyn | CNBC
Customers enter a Chipotle restaurant in New York

On its first-quarter call, Chipotle noted that its carnitas customers love the pork product and appeared to be either dining there less often or not at all until the carnitas returned.

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Bob Derrington, senior restaurant analyst at Wunderlich Securities, called the pork shortage "a meandering negative impact on sales" during a phone interview. "I do think it has had a negative impact on sales. How you accurately determine how much is somewhat a best guesstimate," Derrington said.

Even though Chipotle missed Wall Street's same-store sales estimate, the stock is still surging Wednesday. Shares were up almost 8 percent in afternoon trading.

"The company has dodged a proverbial bullet," Derrington said, adding that "it's somewhat of a relief rally and probably some short covering" after executives said sales and traffic are both positive in July against tough comparisons in Q3 2014.

Not only is the pork deficit hurting sales, it is also getting in the way of price increases that have the potential to prop up same-store sales. In restaurants where carnitas are still on the menu, Chipotle has hiked steak and barbacoa entrée prices by an average of 4 percent to help absorb higher beef costs.

That's helping add another 60 basis points to July sales, but it could bring an even bigger benefit if the price hikes were throughout the country, especially because customers have not shown resistance to the hike yet. So far, the company has avoided raising prices in carnitas-less branches.

"We held off in those markets because we want to avoid the unintended consequence of having customers trade from carnitas to steak or barbacoa and then be forced to pay more for their meal," Hartung said.

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Hartung estimates that when the remaining stores increase prices, "that will get us somewhere in the 100, 110 (basis points) or something like that."

So how long until Chipotle has pork everywhere again?

After finding a new supplier from the U.K. that meets its animal welfare standards, Chipotle said it will be expanding supply during the coming months until it reaches full supply by early next quarter.