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"People won't understand that this company is [taking] an abundance of caution," Cramer said on "Squawk on the Street. " "I think they are going to spend more time in the penalty box than normal."
Chipotle closed 43 restaurants indefinitely in Washington state and Oregon amid an E.coli outbreak, adding to the company's troubles.
"Timing of reopening will be dictated by the progress and pace of the investigation. That is the top priority now," Chipotle Communications Director Chris Arnold said in a statement. He also said that no cause for the outbreak has been determined.
The company on Oct. 20 reported third-quarter earnings per share of $4.59, missing analysts' expectations by 3 cents. Same-store sales rose a better-than-expected 2.6 percent, but they were still sharply lower than 19.8 percent a year earlier.
"That last quarter wasn't that good, they've had much higher wage costs, the same-store sales are back to where McDonald's are and now this, " Cramer said. "These things are very hard to put behind."
Cramer said, however, he thinks Chipotle will be able to move past this, adding that "at some point you'll want to own this."
Bob Derrington, a restaurant analyst at Telsey Advisory Group, shared Cramer's sentiment.
Derrington told CNBC's "Power Lunch " on Monday that he'd advise investors not to sell Chipotle.
"At these levels, the stock is trading almost to a level where it's historically average," he said. "In our view, it's getting much more attractive. There's no doubt about that."
Derrington added that the E.coli outbreak is only concentrated to a small part of the country and that the brand loyalty Chipotle has established with its millennial consumers will bring them back once the outbreak passes.
However, Derrington said the store closures do mean good news for competing Mexican restaurant Qdoba.
Stock in Jack in the Box, which owns the restaurant, was up nearly 4 percent in late trading Monday, while shares of Chipotle were down more than 2 percent.
Disclosures: Cramer's trust did not own Chipotle or McDonald's shares when this article was published.
— CNBC's Ritika Shah contributed to this report.