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Chipotle shares pop after missing estimates

Chipotle restaurant workers fill orders for customers in Miami, Florida.
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Despite Chipotle stock's 5 percent jump on Friday, some analysts are telling investors not to buy. 

On Thursday afternoon, the fast-casual chain reported a 16.6 percent revenue decline in its second-quarter compared to its 2015 second-quarter. 

Chipotle attributed the drop in revenue to comparable restaurant sales. 

"It looks like it's going to take a lot longer if it ever does get back to full strength," Barclays senior restaurant analyst Jeffrey Bernstein said about Chipotle's second-quarter on CNBC's "Power Lunch " Friday.  

Some analysts said that although Chipotle's sales may recover within the next few years, the company's margins will not be the same. 

"You have to differentiate between a good stock and a good business. I think that even the most bearish guys in the world are assuming that Chipotle is going to get their sales back," Wedbush Securities restaurant analyst Nick Setyan said. "Whether it's in 2018 or 2019 or 2020, they will get their sales back, the problem is their margin structure is going to look extremely different coming out of this crisis than going in." 

While some experts were disappointed with Chipotle's latest report, Maxim Group senior restaurant and consumer analyst Stephen Anderson said that there is one thing helping the company right now. 

"The one silver lining that Chipotle has right now is that commodity costs are relatively low, particularly for proteins. Once that starts to reverse, I think Chipotle will get hit harder than the peers," Anderson said. 

Anderson also said that every incremental data point from Chipotle seemed "below consensus."

Bernstein said he was surprised by Chipotle's move, but is still not recommending its shares. 

Disclosures: Barclays Bank PLC and/or an affiliate has recieved non-investment banking related compensation from this issuer within the past 12 months.