This was witnessed on a HealthConnect instance after some unrelated gremlin changed the directory permissions of the git repository, causing every file to be shown as edited. We tried to select all through the Git Web UI and discard the changes, but gotten an "application error" popup. The Application Error Log showed a <STACK> error:
<STACK>HandleRequest+269^SourceControl.Git.WebUIDriver.1 : CSP Error

The resolution was to go into the operating system and run git clean -df.