My dad was like this. He would completely sever ties with a business over any perceived slight by any employee. As a kid, it was quite annoying to not be able to go to a restaurant I liked anymore because Dad once got overcharged for a beer.
From your description, it does sound like the waitress pulled a fast one. But I’d be more inclined to let management know what happened, rather than cutting the whole place out of your life because of the actions of one person.
Also be sure to look for a “sides” pricing spot that usually includes chargers for things like extra gravy ect its usually by where the drinks prices are printed
This is where “Give them the Pickle” came from:
Good story, thanks!
We had to watch that guy’s video (“Give them the pickle.”) at work a few years ago. It’s kind of silly, and the employer has to decide how much discretion to give the front-line employees. If it’s OK to give away a fifty-cent pickle, is it OK to give away something else that costs five bucks? Or what about a fifty-dollar bottle of wine, perhaps when the customer has spent a large amount at dinner? Where is the line?
The pickle?
Those people are wrong. It’s not presuming anything. It’s simple ethics to make clear when there’s an extra charge for something so that there are no surprises on the bill.
I might be able to afford an extra 50 cents for extra tub of ranch dressing or an extra $2.50 to $4.00 (!!!) for a refill of soda, but the waiter should ensure that my choice is an informed choice.
In this particular case, an upcharge is bullshit. This is a Mexican restaurant, and in any restaurant in Mexico, you always get all of the tortillas that you want. Hell, it’s common to send tortillas back because they’ve become cold, and the expectation is that you have enough warm tortillas to finish your meal.
I might say that the upcharge was merited because the OP asked for something called “fajita shells”! 
I dont think the terminology had anything to do with it.
Where I live, ice is often extra. For a while some of us socialized over beer once a week. The beer was slightly overpriced and he ordered over-priced appetizers but got irate about the 50¢ charge for each bucket of ice! (“Ice is supposed to be free.”) I say, “In the city of eye winkers, you should wink your eyes too” — that’s Thai for “When in Rome …”
Something to remember here if you’re on a budget (or not too hungry) is that “pork-and-basil” (or whatever) is more expensive than “pork-and-basil over rice” because you’ll get more pork-and-basil if you don’t say “over rice” — order a bowl of rice separately if you want.
In Thailand?
I agree. It’s not rude at all to mention that there will be a charge for something that a customer requests as either an add-on or substitution. I don’t want to be surprised by seeing a charge for a salad instead of fries, extra tortillas or a drink refill… let me know in advance.
I’d mentally classify tortillas with bread (since they are a form of bread). So I’d be surprised to be charged for extra tortillas, just the way I’d be surprised to be charged for a second basket of rolls at an American restaurant.
But if I was happy with the restaurant otherwise, I certainly wouldn’t make an issue of it.
But if the clientele is mostly gringos, they should adapt to gringo customs. 
ROCOCO: What about my pickle?
DANGER: You’re lucky you still have your brown paper bag, small change!
Or they better be awesome chips and salsa
Yes, I’d mentally classify the tortillas as bread. But are they more like a basket of rolls? Or are they more like an individual dinner roll that comes with an entree, or toast that comes with an omelet? Or are they more like the bun that comes with a hamburger, or the biscuits that come with biscuits & gravy?
In the latter case I would not expect free extras. In the middle case I’m not sure.