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I can duplicate the problem and believe there is a work around.
If the additional behavior "Force polling using workspace" is added to the Git plugin configuration for the specific job, then I can clone my Visual Studio Online git repository from the Jenkins job.
If I don't add the additional behavior "Force polling using workspace", then the job definition page shows the same error as described in the bug report until I add a global credential for Visual Studio Online.
Once I've added the global credential for Visual Studio Online and referenced it in the plugin definition for that job, then the "ls-remote" message disappears on the Linux machine I'm using as master server. It may yet happen on a Windows server.
In each of those cases, I defined a global credential with my Visual Studio Online user name and password, and used that credential in the Git plugin configuration for the job.
I also can avoid that message if I embed the username and password in the Git URL, though that is much less attractive, since it places the username and password in cleartext in the job definition.