E. coli is not Chipotle’s only problem

More pain for Chipotle
More pain for Chipotle

An ongoing E. coli investigation involving Chipotle Mexican Grill is hammering the chain's stock, but the fallout is far from the only headwind the company faces, analysts say.

Chipotle's meteoric sales growth moderated even before its E. coli problems surfaced. Comparable sales growth fell to 2.6 percent in the most recently ended quarter, from 19.8 percent in the prior-year period.

"In addition to risk of a prolonged recovery, sales slowness in 2015 prior to E. coli issues was never fully resolved and could further pressure the trajectory of the turnaround," Cowen analysts wrote in a report.

Since the outbreak reports started trickling in, comparable sales have been down double digits, especially after the CDC expanded the initial scope of the outbreak on November 20.

Read MoreWhy Olive Garden never built a Chipotle rival

Chipotle now expects comps to drop 8 to 11 percent for the current quarter, it said in a filing Friday. If this estimate proves accurate, this would be the first quarterly decline ever for the chain. The news surprised many Wall Street analysts, prompting a wave of downgrades on Monday.

In addition to waning sales growth, Wedbush analysts noted Monday that the chain's throughput—the volume of transactions in a given period—was already declining during the crucial lunch hour. Cannibalization will only worsen, Wedbush predicts, as the chain "approaches unit saturation."

JPMorgan analysts said investors should also be "disappointed" that Chipotle has noted roll out its new ordering app yet, which the chain said would happen in November.

Read More Chipotle stock plummets after chain cuts guidance

"Instead, after a year of delays and still no firm date set for the rollout, we think of the lost opportunity to communicate the facts to Chipotle's most frequent and loyal customer base," analysts wrote.

Despite a wave of price target reductions and rating downgrades since the latest CDC report, JPMorgan thinks the recent turmoil could present an opportunity for investors, particularly with the stock off about 11 percent over the last month and 25 percent over the last three months.

"It's not time to give up on shares. We instead argue that it's the right price to buy," analysts wrote.