I mentioned this in the site's DEV Blog (that I'm... sure no one reads xD). It isn't so much a glitch, as it is a fix to one. To explain in layman's terms, there's a particularly bad patch of code that's causing a lot of issues on the site. It's an in progress fix (that I work on whenever I have the time), but as a side effect of me making changes to it, it's making sub-category counts read zero.
But once it's fixed, category counts will return to normal and a few other problem parts on the site (like the challenges) will also be fixed.
In the future, I plan on just making a mirror of Lunaescence for me to do repairs on, so users of the actual Lunaescence don't have to see in progress fixes as they happen. For now at least, I can assure you that I'm aware, and that it's a necessary step in fixing a lot of the site's problems.