u/R0guefool please help with this
To be clear the patch has not gone live, and we have no made any changes to Smite otherwise. What I assume happened here is that the player has Smite and Flash already then accidentally chose to swap places rather than replace a Smite, or tried changing too late. Though obviously I can't be certain and there is always a chance of a bug, though if this was the case I think it would have shown up much sooner, and more often.
As for the upcoming Smite changes, I didn't work on this system, and don't have all the details, but I believe it just sets your starting loadout to Smite. As the player assigned the Jungle role you could still change your loadout. Like the situation above, where two people swap positions, you would just need to manually do it yourself.