Waiter, there’s a fly in my soup is a common and well known joke (in the UK) This is a variation of that joke the waiter implies they put the flies in the soup on purpose due to lack of fish available. It’s funny because you would expect a polite reply from the waiter but instead he responds that they are there due to the lack of fish.

The joke is that the restaurant put flies in the soup rather than fish as they were short of fish (didn’t have enough fish)

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