In some ways it's obvious: industrial fisheries simply must have an impact on other animals in the ocean given their size and global reach.
I was just reading an article by Ellen Pikitch in The Scientist where she wrote about a study that she was involved in demonstrated that the harvesting of small fish (like sardines) have impacts on sea birds, marine mammals, and other larger predatory fish. The important recommendations from the study included rigorous monitoring of these fisheries and monitoring of their effects on other species that might be influenced by their population status.
What's the lesson for our kitchens? Well, I'd previously written that we should be specifically eating those small, herbivorous fish because they were sustainably harvested (and have a variety of yummy recipes for them). If this advice, however, is questioned, perhaps we must be careful about eating too many of them.
Science is a self-correcting process where we have to be open to changing our minds given new evidence. This might be one of those cases...which, in retrospect, should have been obvious.