When you enter Diffusion and click on a repository, you can normally see the complete directory listing in the "Repository" panel.
Actually, for some older mercurial repositories, the directory listing is not complete (some files and directories are missing).
I am not totally certain if it is because these repos are managed with mercurial since all my older repos are mercurial-based, and I didn't check them all because we have 123 repos at the moment ;-)
And when I write "older repos", I mean "created in Phabricator many months ago".
I can't reproduce the problem as the recently created mercurial repos does list the directory content entirely.
If it can help, my users notify me of this issue for less tha 3 months (our Phabricator instance is updated weekly).
Important notice, the repos in question are actually unalterated on disk, and common clone/push/pull operations are OK, it is just a display issue.