If you are running git under a file system that is not case sensitive (Windows or OS X) this will occur if there are two branches with the same name but different capitalisation, e.g. user_model_changes and User_model_changes as both of the remote branches will match the same tracking ref.

Delete the wrong remote branch (you shouldn't have branches that differ only by case) and then git remote prune origin and everything should work

Permanent Fix

git update-ref -d resolved my instance of this error, e.g.

git update-ref -d refs/remotes/origin/user

Note that this doesn't impact remote.

In my case, a subsequent git fetch fetched that branch again, and following git fetches/pulls no longer gave the error "remote ref is at but expected".

If that doesn't work, a temporary fix:

Note also that if you don't care about the branch in question (e.g. you just want to update master, not origin/user), a git pull workaround is to fetch then just merge the particular branch you care about, e.g.

git fetch # may give an error for a particular branch, but other branches will still be successfully fetchedgit merge origin/master

Just delete the folders and files under \.git\refs\remotes\origin.Works, when u don't have unpushed changes.