This is not a BUG, this is just how Odoo is designed to work.

You might need to expand your understanding of the difference between a product template and a product variant.

https://www.odoo.com/documentation/user/11.0/inventory/settings/products/variants.html 

https://www.odoo.com/documentation/user/11.0/ecommerce/managing_products/variants.html

Once you create Variants from a product, that original product becomes a product template for the variant (a place to edit the attributes common to all variants) and can no longer be sold.

The variants of that product are now what is sold, so that's why only they have an internal reference.

Example:

If you create a product called 'TSHIRT' and then create two variants 'WHITE TSHIRT' and 'BLACK TSHIRT' then you no longer sell 'TSHIRT'.  You now sell just the two variants 'WHITE TSHIRT' and 'BLACK TSHIRT'.  The 'TSHIRT' remains the template for both variants, and any new ones you may create.  The product template is where you manage the information common to all variants.  The product variant is where you manage the information specific to that variant.