You can make a new file under [.git\refs\remotes\origin] with name "HEAD" and put content "ref: refs/remotes/origin/master" to it. This should solve your problem.
It seems that clone from an empty repos will lead to this. Maybe the empty repos do not have HEAD because no commit object exist.
You can use the
git log --remotes --branches --oneline --decorate
to see the difference between each repository, while the "problem" one do not have "origin/HEAD"
Edit: Give a way using command line
You can also use git command line to do this, they have the same result
git symbolic-ref refs/remotes/origin/HEAD refs/remotes/origin/master