No, I haven't while mystery shopping.
However, I have worked in restaurants for quite a few years. There, it is a standard practice to discount part or the entire meal for restaurant mistakes. The idea is to pay to make the customer happy. Another way of saying it is to pay for the customer not to bad mouth the restaurant. Restaurants rely heavily on word of mouth to survive. So it works for them.
Allergies are a potential problem for folks that are deathly allergic. They don't want the bad word of mouth that you could be spreading. As it was no biggie for you, I guess you are only mildly allergic to them.
If it happened on a shop, I would wonder how to get a proof of visit for the MSP.
Happily shopping Rhode Island and nearby Massachusetts and Connecticut