It isn't completely clear if you are looking for a technical, industry term or for a metaphor or idiom.
The industry term for the excess fish is Bycatch defined on Wikipedia as:
Bycatch, in the fishing industry, is a fish or other marine species that is caught unintentionally while catching certain target species and target sizes of fish, crabs etc. Bycatch is either of a different species, the wrong sex, or is undersized or juvenile individuals of the target species. The term "bycatch" is also sometimes used for untargeted catch in other forms of animal harvesting or collecting.
Sources which talk about bycatch don't seem to use a single term for the 'whole phenomenon... in which for sake of one the whole lot has to suffer', but do speak of fishing methods being 'non-selective' or 'indiscriminate'.