Azure Pipelines - Git checkout step fails with cannot lock ref error

For one of our clients, we noticed their builds started failing at the checkout step. Looking at the logs the error was error: cannot lock ref 'refs/remotes/origin/ ': there is a non-empty directory '.git/refs/remotes/origin/ ' blocking reference 'refs/remotes/origin/ ' In this post we will see what was the root cause and how to fix it.