My parent directory filename contains exactly 2 spaces!
As of 2014-11, GitHub:
does not list it on the tree show
shows up internal files normally with /%20%20/README.md
relative links in markdown fail and link to the parent directory instead: a.md
if you try to to view it with /%20%20/, shows the parent directory instead instead of the directory, but the breadcrumbs still correctly show as a subdirectory: