Missing files from repository after recent commit

Sometimes when I push a commit to the master branch of my repo, newly added files will be missing from my repo. And those that do show in the list of files, are not found.

When I return to the list of files and reload, then I'm shown an outdated list of files even with the master branch selected. It seems completely random.

I've already tried logging out and clearing my cache. Neither solves the problem.

Edit: It appears I can view the missing files through the commit history, just not from the branch file listing.