Stopword removal (suprisingly) decreases accuracy of naive-bayes model

Stop words typically remove such things as "a, an, the, it". Often this can be beneficial when we are classifying based on topics, which are well described by nouns and adjectives. However some text classification tasks are more abstract. Consider classifying fiction and non-fiction articles on the same topic, what would the difference between these two writing styles be? They would probably use the same nouns but what about the frequency of "the" vs "an" or "he" vs "they"?