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​Chipotle customers ask: "Where's the pork?"

Americans have turned to Chipotle Mexican Grill (CMG) to fill up on humanely raised meat and premium ingredients, fueling its fast growth. The only problem? The Mexican food chain is coming up short.

In January, Chipotle dropped one of its pork vendors after discovering it wasn't keeping the chain's strict standards for responsibly raised meat, which meant one-third of restaurants couldn't be supplied. Three months later, the restaurant company is still searching for a solution, which spokesman Chris Arnold noted isn't all that easy. In the meantime, some customers are taking to social media to complain about shortages and missing ingredients.

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The lingering pork shortage at Chipotle illustrates how difficult it is for major chains to reliably source humanely raised meat. At the same time, consumers are increasingly buying organic food or naturally raised meat, putting pressure on fast-food restaurants such as McDonald's (MCD) to upgrade their offerings.

Fewer than 5 percent of pigs raised in the U.S. meet Chipotle's standards, Arnold told CBS MoneyWatch. The restaurant is also investigating using other cuts beside shoulder for its carnitas, the shredded pork that fills its burritos, but that adds in complications of price and taste, he said.

"There are no quick fixes for it," Arnold noted. "There isn't a switch you can throw and serve all organic veggies and all humanely raised meat at our size and scale."

The bottom line: Chipotle doesn't know when it will be fully supplied with carnitas again. The chain is coping by rotating supply between locations, so that all restaurants can serve pork at least part of the time.

In the meantime, the competition is muscling in on Chipotle's game. McDonald's has vowed to start buying beef from sources of verifiable "sustainable meat," while Panera Bread touts its use of chicken raised without antibiotics.

The ingredient shortages are raising alarms with some analysts, Bloomberg News reported. Chipotle's expansion, which will include as many as 200 restaurants this year, might be hampered if it can't solve its pork problem, Motley Fool analyst Asit Sharma told the publication.

"The company may be forced to slow its store growth if it can't evolve new relationships with 'sustainable' suppliers quickly enough," Sharma said.

Chipotle disputed that, with Arnold calling it "ridiculous" and adding: "Availability of ingredients isn't a determinate" in opening new restaurants.

Some customers aren't all that understanding of Chipotle's growing pains. A common complaint on Twitter from is that restaurants have run out of an ingredient. "I don't I understand why the Chipotle I go to always has a sign up about something they've run out of," one patron griped on Twitter last month.

Guacamole has become another trigger point for customers. Earlier this year, the chain warned that it could temporarily suspend serving guacamole or other items, depending on fluctuations in ingredient prices, setting off concern among Chipotle fans. While the chain hasn't cut off the guacamole, it does charge extra for a serving.

Chipotle's pork struggles result from its policy of buying only from farmers whose pigs are raised outside or in "deeply bedded pens," instead of the factory farms that supply most of the country's meat.

Those guidelines mean farmers need barns that are twice as expensive, and the pigs can require much more time to care for, Bloomberg noted. About 70 percent of domestic pork production comes from big meat processors that don't meet Chipotle's standards.

"We want to fix this pork thing," Arnold said. "One way or another, we will get this done."