Yeah. It's always the words you don't suspect that make the editor rip out his/her hair. ("If this guy uses pusillanimous one more time I'm setting fire to the manuscript!)
The program should overlook certain categories of words (conjunctions, articles, pronouns, the protagonist's name, etc) but I see this more as a "don't bother with these" list. Or, would you prefer that Storyist be able to know a conjunction when it sees one?
-Thoth.