The issue you are facing could be the result of un recommended way of deleting the associated resources to the VM. You may also try a different way to delete the VM as given in the following steps
- Login to https://resources.azure.com/ portal
- Browse the exact location of the virtual machine as shown in the following example
- Click 'Edit'. Click 'PUT' button to update the VM
- Try to delete the VM again from azure portal and see if it works. If that also doesn't help, click 'Actions (POST,DELETE) Button from the resources portal
- A 'DELETE' button should visible as below and try a delete by pressing the button
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