Chipotle does not have a gluten free menu but instead has a list of gluten-containing ingredients to avoid. Cross-contamination is a concern, however, so let the person taking your order know that you are gluten free and if you need them to take the proper precautions.
From their website: "If you avoid gluten, don't eat our flour tortillas. If you are highly sensitive to gluten and would like us to change our gloves, just let us know at the start of your order. You should be aware items containing corn, including corn tortillas (chips, soft corn, and crispy corn tortillas) and corn salsa, may have a small amount of gluten from potentially co-mingling with gluten-containing grains in the field."
I ordered chips and guacamole and asked if they could scoop my guacamole from a fresh container to prevent cross contamination. Initially the young man agreed but then an older gentleman who was his boss raised his voice and refused. I did not want to risk getting sick so did not eat here. The older man raising his voice was rude and embarrassing.