“Free” is a relative term, as Chipotle uses meat and dairy products fed GMO feeds.
Unless that animal feed can be proven to be mutagenic(good luck with that), I don’t see a case that could be made on that.
The drinks, though… If Chipotles ads are simply saying GMO free, and the information on drinks is shoved into a mention on their website… There might be an argument regarding false or misleading advertising.
Easily fixable with fine print in ads such as “While Chipotle prepared and branded items are GMO free, items provided by other vendors, such as soft drinks, may contain GMO”. If their ads already include such a disclaimer, though, then there’s no case at all.
Of course, the whole anti-GMO thing is based on nonsense. There’s some reason to distrust Monsanto, but the basic science and the GMO foods that actually enter our food supply(there is, actually, testing) is all fine. Still, if you’re going to claim GMO free, you have an obligation to actually be GMO free and/or make sure your advertising is clear about an exceptions to the general policy.