That is in a large part because atlantic salmon (the primary kind in net pen aquaculture) are usually genetically modified. The modifications improve their growth rate in aquaculture net farms, but are probably not that great for a wild fish. So when these fish escape and those genes contaminate the wild fish, it might be a bad thing. But no one has ever really studied how bad, I think. Sometimes escaped fish amount to a large part of the population, and that can be bad just from the standpoint of losing natural genetic diversity because these fish come from a smaller number of parents than wild fish. In aquaculture, it is possible to get a much higher survival rate on the young than in the wild, of course, so you don’t necessarily spawn as many adults.
With Pacific salmon, many fish are spawned in hatcheries to supplement the wild fishery, and not grown to harvestable size , and are released at different levels of growth depending on circumstances. (although some of these fish, most of the ones that survive to spawning, return to the hatcheries where they were produced, and are harvested there, in part to get the eggs for the next batch of fish). Many of those carcasses are taken up to where the fish would have spawned if there were natural runs, and thrown in the water to decompose there. )By that time, they are not great eating anyway) The idea is to recreate this natural source of nutrients that run the stream productivity. In the past, there has been a problem with genetic diversity from this process, because the only spawned enough fish to produce the number of young they needed. Now, however, they are more careful to maintain the genetic diversity and arguably they are taking care of that problem by spawning more fish. There are studies that are done that indicate how many fish need to be spawned to maintain the diversity. I’m not up enough on the current debate to know how well that problem has been taken care of.
I forget if it was mentioned before, but other problems with salmon net pen aquaculture are 1) the amount of poop and uneaten food that ends up in the area, causing problems similar to those you’d expect from a sewage effluent, and 2) antibiotics and therapeutics added to the water and food, which end up in the environment. In the case of the antibiotics, it is a problem of generation of resistant bacteria.