Coli that are the cause of so many meat recalls and the death of many children and adults. Cows will normally shed all bacteria if their diet is reverted back to grass and if they are allowed to roam free in the Field they will be happier and fertilize their own manure so there won't be the need to haul the manure they produce to some other area or dump it in the water. It seems the entire system is skewed to produce the most amount of the food in the least amount of cost without any respect for the animals, the environment or even the consumers that are paying to eat that food. .
The second problem in the movie that we have seen the overgrowing of Corn. Corn is a staple of American diet and it's grown in such mass quantities now not because we eat so much corn but because it's a cheap grain to produce and it's the major food source of all the animals that are raised for our needs in the U.S. The corn produced in the US is genetically modified (70 percent) and it's added in clever ways to each and every processed food in the supermarket. We have so much corn that we came up with uses of it from high fructose corn syrup to maltodextrin and also lactic acid, citric acid and countless others. The same is true for GMO Soybean that's used in canned food under names like bulking agents, carob, guar gum etc. If instead of growing so much corn we were growing natural food and grass then these problems wouldn't arise. Corn is used in so much quantities that it is also becoming a staple diet of farmed fish, we are teaching the fish to eat corn. .
The third problem we saw is the control and regulation of the meat processing plants. The plants practice such unhygienic ways and the animals could be ill or have any disease they are still processed. Many times the workers contract bacteria on their hands that their fingernails separate from their hands and they also get antibiotic resistant strains of bacteria systemically, the workers work in poor conditions and are mostly recruited from Mexico and other poor countries, and are usually farmers in their countries who went out of business when they couldn't meet the price of cheap American food.