We once got an entire meal comped, and for less than this (a rude waiter, we ordered chicken with garlic but it came without and then were told "they don´t put garlic on chicken", food took too long and then a film crew came and set up lights next to us, without even asking).
In the moment, NOT at the end of the meal, we asked to speak with the manager and said we were very upset for the following reasons and did not want to pay for the meal. The manager, suprising us, said we were right and comped the meal and offered anything we wanted on the house--we didn´t take advantage of that offer, we just finished our meal and left, and left a tip, even though the waiter WAS the problem. (I was with my Argentine husband so you can assume that rude was rude by standards here).
If a nail is in your meal, you should stop the presses and leave or ask for the meal to be comped at that moment. When you assume that you will be comped or that they should take off the cubierto charge that is when you run into trouble, because that is what you thought in your head that was correct, and the restaurant owner in his head thinks he did more than enough. And by staying you show that is not a big deal.