Pretty simple recreation.
I have my code menu open, and it has one query hightlighted.
I also had clicked on a component.
I did the duplicate shortcut (cmd + d) - and both the component, AND the query get duplicated.
What I've noticed - if you click query, then component, then cmd + d - both are duplicated.
BUT if you click component, then query, then cmd + d - only the query is duplicated.
ETA: Turns out, that even if you have the "Component Tree" open, if you have ANY query open, it will still duplicate the query AND the component.
…this explains the mysterious duplicate queries I was seeing created and not knowing how I was creating them.