I just created a repo and added some content as described here: https://writequit.org/articles/getting-started-with-git-annex.html

Some of the directories I added ended up fine, while others have lot's of broken symlinks.

git annex fsck file

gives me :

** No known copies exist of file
git-annex: fsck: 1 failed


git annex get file

gives me:

get file (not available) 
  No other repository is known to contain the file.
git-annex: get: 1 failed

The objects directory is about the same size as the repo was before I annexed it.

Any ideas on how to troubleshoot further?