This is something of a "magic words" question. This means that you are asking for the words that people say in some situation. The fact is that (with a few exceptions) there are no magic words. Any communication is a dialogue. So it is vitally important that you consider not only what you say, but what the other person is saying, and respond to that flexibly.
Can I help you?
Yes, I think there's a mistake on the bill (or check in American English). You charged one pizza less.
Let me see
Yes, we ate four pizzas, but we were charged for three pizzas.
Oh thanks for pointing that out, it very honest of you!
etc etc etc.
The actual phrase "You charged one pizza less" is not idiomatic, but look at the dialogue, communication is occurring. It doesn't really matter that the grammar is wrong in that part because you are talking with someone, and not just spitting out a fixed phrase.
Better would be "You've charged us for one less pizza than we ate" (the present perfect is indicated as we are talking about the effect of past actions on the present). But this can only function as part of a dialogue. The important thing is to listen and respond.