For me I tracked down the source of this warning to much earlier when I incorrectly issued an “update-ref” command. If you forget to specify the full refs/heads/mybranchname path in the first arg, then a file .git/mybranchname gets created, which later leads to this warning when you try to switch to that branch.
It is solved by simply deleting the .git/mybranchname, eg:
rm .git/master
And for reference, the correct form for the update-ref command is:
git update-ref refs/heads/mybranchname mytargetbranch
Don’t forget the “refs/heads” part!
Also, my most common use-case for update-ref is simply manually moving a branch to point to another commit, which I’ve found a simpler syntax to do:
git branch -f myBranchToMove destinationBranchOrHash
This syntax is easier for me because it doesn’t require that error-prone refs/heads path qualifier.