Exterior contamination.
I've butchered thousands of animals (mostly poultry) but also cattle, sheep, goats, pigs, deer. etc.—never in a factory setting.
It's impossible (or nearly impossible) to not contaminate the carcass in some way especially when removing the digestive tract and hide.
Ecoli and salmonella get the most attention but there are other pathogens of concern (brief list, see reference below for much more extensive information)—some of them could be lurking in the digestive tract or nearly anywhere on the outside of the animal.
Good reference: The USDA's Bad Bug Book, Foodborne Pathogenic Microorganisms and Natural Toxins Handbook, 2nd edition, 292 pages.