A part may fall on the floor, be picked up and put back into the process again without being properly cleaned. Lastly, the final packaging materials, cartons, etc. can be contaminated by previous fruit or tainted water, by being set on contaminated ground tainted by manure, or by being transported in a vehicle that previously held animals. As long as they weren't grown in raw manure, you might think sprouts would be a relatively safe form of produce. After all, they can be grown effectively indoors. Yet indoor growing conditions of sprouts can be substantially less than sanitary.
Epidemiology points to the source of at least one outbreak as being the seed itself.
Alfalfa as a crop can be fertilized with raw manure. A combine is then used to harvest the grass and seed, whipping up a considerable amount of the soil in the process of harvesting. Thus, a seed which might otherwise not have come into contact with animal feces, could easily become contaminated. The challenge with sprouts is that the growing conditions that foster sprout growth are ideal for escalated bacterial growth. For approximately 3 days, sprout seeds are warmed, kept moist and given a lot of light in order to encourage growth.