The VMInstance concept was introduced with VM-Centric Backup Operations for VMware two years ago and individual VM's had their own Backup Job Id's. You used to have run a workflow convert an empty VMware client to the V2 Index. In recent months this has become the default.
Now VM clients will appear in the console UI and this can result in some clutter, but like most of Commvault - there is an option to not show the VM's from your view all the time.
From the Commvault Console Ribbon, click Control Panel -> User Preferences -> Client Computer Settings -> Show Virtual Machines. Un-tick this box. Note, you don't need to restart your client and you can put it back at any time.