sphinx-apidoc ignoring some modules/packages

While working with the awesome documentation tool Sphinx, I ran into a situation where I could not seem to make sphinx-apidoc to recognize modules under a subdirectory of my project. I triple checked my command but it was fine. The same command worked properly in my other project where it located all the files under a package and created documents for them all. However, this time it seemed to be refusing to recognize and create documents for only a few subdirectories(packages). I found it hard understand what could possibly cause this bizarre behavior all of a sudden.