A book in a calibre library - i.e. a line on the book list -- can only have one file of any format - i.e one EPUB, plus one PDF, plus one AZW3, etc etc. But not two of anything. That's not going to change any time soon - if ever.
I had completely forgotten, or more likely never even noticed that the Metadata edit screen had that Add format button, I add formats with cut and paste into the book list
BR