To re-itterate what starvenger said, I'll take it up a notch.
The McDonalds in Welland, Ontario (aka shithole) will refuse to put a customer request on anything. I went and ordered a Double Big-Mac the one day and I asked if I can have Ketchup on the burger. The person said they couldn't do that because they don't allow that condiment on it. I talked to the manager who is younger than me, and the policy is that they don't allow condiments that they don't put on certain sandwiches and other items on their menu.
This is the only store that I know of that does this.