Hello there,
The right channel would be to raise this via the feedback hub so that the Microsoft team can have a look into this. Meanwhile, you can share the error message generated when you run the Get-MsmqQueue to Remove-MsmqQueue so that we can have a look into the error code. Build a cleanup feature and add a queue by creating scheduled tasks on a remote computer to call a script created with the command and see if that helps.
You can raise feedback to the Microsoft team. The Feedback Hub app lets you tell Microsoft about any problems you run into https://support.microsoft.com/en-us/windows/send-feedback-to-microsoft-with-the-feedback-hub-app-f59187f8-8739-22d6-ba93-f66612949332
Similar discussion here https://social.technet.microsoft.com/Forums/windows/en-US/bec1c074-a650-43d0-b325-55e5e2d2554a/getmsmqqueue-cmdlet-is-throwing-object-not-found-exception-in-windows-2012-r2?forum=winserverpowershell
Hope this resolves your Query !!
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