Any population is bound to have some less fit individuals which would quickly get weeded out in nature as they are simply not competitive enough to survive. In a farm where they are protected from predation and practically hand-fed, poor fitness members at least can survive, though probably not thrive (obviously). I'm guessing it's probably just not cost effective to sort and cull them early on.
That video is edited to imply that the pen is nothing but deformed sickly fish which may or may not be the case. Is the proportion of sick individuals higher here than other farms or broods? If so, then maybe that's something worth investigating then, and indicative of a more serious issue. Not trying to accuse anyone of anything, but maybe they just shot video of the worst examples they could find for shock value, without providing any context. It's hard to know...