How do I handle a situation where a waitress at a sandwich shop clears my food when I am not done?

If you are going to continue to frequent that restaurant, then yes, I would worry about it. Both you and the waitress made a very huge scene together over a simple misunderstanding. i don't think that the exchange that you had with each other was necessary, and she obviously took it too far. my advice would be to find another place to eat.