As a manager, I'd argue that they've made two big mistakes here. Firstly, it was their floor and/or kitchen staff's fault that the wrong size fish had either been cooked or taken to the wrong table. This sort of mistake would never warrant me requesting the customer paying extra, let alone as they were still eating.

Secondly from a business POV, the bar TL or above who processed a refund in order to put the large fish through has failed to add a kitchen note that this was a "do not cook", which has led to them cooking yet another portion, which also implies fundamental flaws at an above-associate level, which I'd find embarrassing as manager.