This is definitely an issue, imo. I've got a bunch of workflows called "XYZ Bookmarks" (Firefox Bookmarks, Pinboard Bookmarks etc.), and Alfred considers none of them to be matches for the query "bookmarks".
The preferences search stands out in particular, but I think this is generally an issue with Alfred's filtering outside of its default results. There, it does a fantastic job of learning and adapting to my own usage patterns. In most other places, I have to adapt my usage to suit Alfred instead because its matching is so strict.
You can't search both track and artist fields in the iTunes Mini Player, which is a very natural way to search for something like a song (the iTunes library is such a perfect fit for a SQLite database with FTS, too). I can't select my "Rename for Web" File Action with "rw" (or "rfw" or "renweb" or anything that isn't the start of "rename" or "for" or "web"). I can filter to "Application Support" with "as" when I navigate to ~/Library, but that also matches a bunch of other folders, and a more precise query like "appsup" (which is what I would naturally use) doesn't work.
I don't expect (or want) full-on fuzzy search everywhere, but it's a perfect fit for File Filters, and Navigation Mode would benefit greatly from being more flexible, too, imo. I want Alfred to learn from and adapt to me, like it does with its default results. Currently, Alfred's strict filtering means it's the other way around.