What kind of flour are you using?
cut in shortening (butter or canola oil)
Shortening is partially hydrogenated vegetable oil aka Crisco, not butter or canola oil. Which are you using? I don't think butter will work that well in a tortilla.
Besides that, ingredient wise, you seem to be alright. Your process intrigues me.
Do you add the water first and then cut in the shortening?
And the light brown spots that form are on the bottom, correct?
What kind of pan have you been using?