Sounds to me like the manner in which you placed the order was confusing to the employee. You wanted a Whopper with no pickles or onions and a medium chocolate shake. Why didn't you just say that instead of talking about cheese and french fries?

The fact that you didn't take the time to address your issues with the manager at the time it happened tells me that it just wasn't that important.

There's no way you deserve to be reimbursed.