That's not what they're claiming, they're saying that if ingredient prices rise (e.g. for avocados) Chipotle can raise menu costs to protect margins. Nowhere is it implied that guacamole was being sold below-cost.
I don't understand what the confusion is: the article says they do less well financially than they would have if their ingredients were cheaper. The original comment here says "but they can always raise their prices" but that cannot guarantee that they do well financially. If the article had claimed that their margins were too low or that the extreme that they were losing money from each sale, then the first comment would have made sense. But it doesn't.
>>Some restaurants were forced to add a surcharge on guacamole, or temporarily to scrap it from their menus altogether. Others swallowed the bill.
They could raise prices but they have chosen not to so far. They may have to in the future. That explains why their financials were not great.
> Chipotle, a Mexican-themed restaurant chain, said that “historically high avocado costs” were a big reason why it posted disappointing financial results last year.