Apparently there's a config in git that manages which origins should it fetch.
So if for some weird reason your git fetch is not fetching the remote refs you expect,
Check your git config
git config --get remote.origin.fetch
it's probably something like
+refs/heads/master:refs/remotes/origin/master
instead of
+refs/heads/*:refs/remotes/origin/*
You can change it to fetch all refs and heads with
git config remote.origin.fetch "+refs/heads/*:refs/remotes/origin/*"