The most worrisome sign for Saleh is that recovery in several regions is lagging.
"We view the fact that sales in the West Coast and Northeast remain in the negative low 20s and high teens, respectively, on a sales-dollar basis as evidence that recovery remains anemic," Saleh said. "While we are encouraged to see a more pronounced improvement in the Midwest and Southeast, we don't believe this will be enough."
The Northeast was one of the areas most affected by Chipotle's food safety incidents and had rebounded slightly in January. Saleh said that weather was a factor in the lackluster growth in the Northeast during the first month of the year, but that "sales levels are still suffering from the steeper decline early last year."
Baird analyst David Tarantino said he hesitates to conclude a "material sales recovery is underway at this stage."
Chipotle's management team has a "good game plan" for the future, Tarantino said, citing the chain's improved guest metrics in each of the last six months. However, a possible credit card data breach could pose a risk for Chipotle's sales recovery, he said.
The burrito chain told investors during an earnings conference call Tuesday that it had detected "unauthorized activity" on a network that supports payment processing for purchases made at Chipotle restaurants. The company said it believes it has taken the proper steps to stop the activity.
"This issue may bear watching, as — at times — similar issues have adversely affected same-store sales trends at some of those restaurant concepts unfortunate enough to go through this challenge," Mark Kalinowski, a Nomura-Instinet analyst, wrote in a research note Wednesday.
At the moment, there is little information about the scope of the unauthorized activity.
Chipotle's stock has whipsawed since the earnings release, first rising more than 6 percent on the company's better-than-expected earnings, and then erasing those gains after it revealed the payment systems issues.
On Wednesday, the stock closed up more than 2 percent.