This actually happened to me twice. I beat a top 50 opponent who had nothing but Quantum Towers, but when I won the spin, the card I won was a non-upgraded Quantum Pillar.
Since it has been explicitly stated that the slot-machine-roll upgrades come from your opponent's deck, I assume this is a bug, since there were no Quantum Pillars in his deck.
If it's not a bug, but is instead intentional behaviour (because "you can only win upgraded cards from fighting false gods" or something like that), then I would assert that this is very lame.