I love me some burritos, however my major gripe about Chipotle is the god damn cilantro they put in just about EVERYTHING.
Cilantro is nasty. It smells like unwashed ass, and tastes like metallic liquid hand soap. If they didn't put this crap in 3 out of their 4 salsas, and even in their rice(!) they'd easily get 5 stars... I'm tired of getting strange looks from the staff when I refuse to eat the rice they have loaded with this foul weed (yes, cilantro is a WEED, not an herb... get it right), when they have to go get the regular rice they hide near the stove that doesn't have it in....
Otherwise it's clean and the staff is mostly friendly. Their outdoor patio needs to be wiped down a bit more often though, especially with the nice weather lately.