Man, it ain’t the beans, it’s the peppers and/or spices.
Seriously, I’m not fucking with you. Beans are great insoluble fiber, and they reduce the effect of the other ingredients to some degree. This is a widely used way for IBS sufferers to reduce the impact of the effect. Extra beans, as long as you aren’t sensitive to the beans themselves (which is a thing), or added dairy (again, if that isn’t a trigger for you), and doubling up the tortillas all help to some degree.
If the dish is also fatty, that’s going to end in your end not ending well. Since what a lot of people think of as “Mexican” tends to be like what you get at Chipotle or Taco Bell, the fattiness is assumed.