How that happened I cannot answer!
To achieve the same I would- Select all images, press CTRL+' (the key with quote symbols) three times.
To view only the VCs (to delete?) you can filter for 'Attributes' and there is a toggle icon to show only VCs to the right of flags, stars, colors, etc.
You will need a smart collection to filter for VCs that have NOT been edited.
Have successfully removed 3576 VCs and retained edited VCs.
bonus is now knowing more about smart collections & attributes.
Still do not know how I did this but I was working with print templates at the time, and saving templates & collections.
Am pleased you have found the fix.
An idea- when ever a collection is created you can check the box to create VCs for all the selected images being added to the collection. If you created multiple collections with all images selected and the "Create VCs" was ticked, then, yes, you would create multiple VCs with each collection.