I worked at a burrito place as a second job for a while... the "change" in the meat recipe was probably the addition of textured vegetable protein (TVP). A lot of places use TVP as a filler. It really doesn't have much flavor of its own and before its cooked it looks a lot like dry dog food. They could also be using "autolyzed yeast extract" or "hydrolyzed protein" too, and since MSG is a byproduct of making hydrolyzed protein, when they include it in the recipe they don't have to list MSG in the ingredients. Other than the possibility of MSG, TVP and autolyzed yeast are completely safe to eat, similar to tofu in texture... I have vegeterian friends who eat them all the time.

I've never eaten at Chipotle so I wouldn't know for sure whats in their stuff. Most places I go I get chicken, steak, or tofu and don't bother with mystery meat.