Traceability was likely working not too badly, they just kept finding eggs that lead to other ranches and therefore had to keep recalling. As far as it only affecting a few hundred layers would depend upon biosecurity between their ranches (workers getting it on shoes and taking it to another ranch and spreading it, a poor sanitary practice). If the FDA saw this practice, they likely included more ranches as a precaution until the flocks can be fully tested and environmental swabs taken to see where all the bad bugs are hiding.

Also, most commercial hens do lay an egg daily because they have their "daylight" artificially adjusted to promote more frequent laying than a bird does naturally.