Which of the violations of the chicken farms in the salmonella case is considered the problem?

The FDA sited the chicken farm responsible for the salmonella outbreak for the following violations among others:

I take exception to your thinking that these violations would be common with organic/free range eggs. Uh uh. Rodents and flies are due to poor sanitation which is a big no-no. Wildlife is never allowed access to chickens unless you want to get up in the morning to a lot of dead chickens. Wild birds flying in and out is a problem because they can carry viruses but even free range chickens are usually housed/sheltered. I mean you just don’t want vermin and wild animals and birds mingling with your chickens no matter how they’re being housed. Free range doesn’t mean they’re allowed to run wild in pastures like horses and cows. It means they’re cage-free and get to run around on the ground in large pens. The key to producing good quality free range eggs and chickens is not to crowd them. Ideally, all animals we use for food should be well/safely housed, provided with enough room to move around freely, provided clean food, water and, for chickens, nest boxes and cared for properly.

The feed was contaminated on the farms with the outbreak. It might have been contaminated by the feed producer or been contaminated by wildbirds or, depending on the kind of wildlife moseying around the place, by the wildlife. The scientists will have to collect a lot of data to determine the source of the salmonella…although it’s a fairly common bacteria in reptiles and birds.

Caring for Parakeets : Health Problems in Parakeets