Although I haven't done this in a few years, this still works in plenty of places:

Call first, and explain how the fast-food place mangled your order*. Ask for them to replace the missing Quarter Pounder or whatever. When they agree, leave your name. Then, go there and collect!

*There have been numerous times when I really was shorted but didn't bother to try to get it corrected. This makes up for those times- if you need justification.