yes, as AndrewTilley mentioned, the new default bindings are… strange. It is so hard to mentally arrange the buttons, and they are all over the place on the controller instead of in groups. Also, changing the potion button was an odd choice.
To me, it makes much more sense to have the controller buttons like so:
Left (X or Square) - Flask
Up (Y or Triangle) - Ability
Right (B or Circle) - Ability
Then L1+R1 Bumpers can be the other two abilities
Leaving minion attack to L2 (Left Trigger)
And primary attack on R2 (Right Trigger)
This lets you press all 4 abilities easily, and is simple to memorize.
Like example, decoy and smoke mine on Triangle and Circle lets me push both at the same time, this is difficult with the default bindings because they are on opposite sides.
Anywho, he nailed it on how to reproduce the issue, I left my controller plugged in instead of turning it off, and when I restart the game it was still the same bindings.