The two prominent dilemmas that the film address is that of logistics and morals; industrial farms simply are unable to feed America because of how they feed their live stock and the farmers mistreat their animals in a medical sense as well as moralistically.
Joel Salitin explains that "Part of our responsibility is to respect the design of nature," and that when we feed Cows other dead cows we are mistreating the general construct of life. We also see many instances in the film where you need to treat for illnesses and bugs that are otherwise unnecessary in organic farming.
70% percent of farming that produces crops such as corn and soy beans goes to feeding the masses of animals to produce second-rate meats and secondary products like eggs and milk. 30% percent goes to immediate consumption. Salitin muses what we could do with the 70% percent if it did not go back into production of industrial farming knowing that it could make a huge difference in the sustainability of America. According Cornell University, "If all the grain currently fed to livestock in the United States were consumed directly by people, the number of people who could be fed would be nearly 800 million." That is an unprecedented amount grain that could heavily impact our society as we know it if only we can refocus are resources and re-purpose the mass industry farming.