Cutts: Yea, it is also important to realize that there are many many algorithms, maybe the majority of the algorithms that don't have any exception logs.
And even though this comment came from Bing's Sasi Parthasarathy, I'm pretty sure it would apply to Google's process, too: "But the interesting part is that any time we have these static overrides, we will make sure that the next iteration of the algorithm actually handles these lists. So these lists are constantly evolving."
Here's how I envision it working. In the early days of the hidden text algorithm, sites used to trip a false positive because the page had a white background but the text container had an image background. They logged the exceptions and then upgraded up the algorithm when they had the data and a approach that worked.