Picking the coffee at the right time
Near the end of the harvest, coffee that isn't quite ripe is stripped from the trees to make way for the next year's crop. These beans are still usable, but far from ideal, and generally get lumped into a scary-bad category called "subgrade."
Whether the coffee has been water quenched
In extremely large-batch roasting machines, there's so much coffee cooking at once that you can't air-cool it; it needs to be hit with a quick squirt of water inside the roasting drum. There isn't great data on this, but many roasters believe that even though the water evaporates almost instantly, it decreases overall quality if water comes into contact with the beans.
Prioritization of quality or consistency
In order to scale as a roastery, you eventually have to sacrifice quality for consistency. When you're roasting 2 million pounds a week, it's hard to focus on the nuances.