Files missing from a git clone

So here's what happened:

On machine A, I cloned a shared git repository. Then I started a new branch, added a directory with a bunch of files in it, committed, and pushed the new branch.

On machine B I then cloned the same shared repository, created a remote tracking branch for the new branch I'd pushed, and pulled.

Somehow, certain subdirectories of the directory I added at A didn't show up in B -- even though other subdirectories, ones that were added in the same commit, did.

Going back to A, I tried to git add the directories that didn't show up. Nothing happens. I tried git log on those same directories -- the output is empty.

Any ideas what happened, and how I can fix it?