They messed it up by porting the exact same button layout to every console.
Take a look at where the B and A buttons land on an Xbox.

TRIGGER WARNING: DISSENTING OPINION

If the discussion here is to be believed, there is some serious hypocrisy going on here.

The problem here is that the A and B buttons are mapped contrary to the convention, and everyone is calling it a big deal, even though an option exists specifically to fix it. Yet Shovel Knight has the same problem, with a similar fix, and I haven't seen a single complaint about it regarding that game.

And I know why.

It's because Mighty No. 9 is a Bad Game, and Shovel Knight is a Good Game.

I won't say that these reputations are entirely undeserved, but they are definitely exaggerated. Bad Games are irredeemable; their positive qualities are downplayed or outright ignored, while the spotlight is shined on their negative qualities. The reverse is true with Good Games.

When we discuss a Bad Game: "Problem X is one of many issues that plagues this game! It doesn't matter that it has Solution Y, it shouldn't exist in the first place!"

When we discuss a Good Game: "Why are you even bringing up Problem X? It has Solution Y, and that's one of many things that makes it a great game."

…even if the issue exists on exactly the same scale, or if it's worse in the Good Game. That doesn't matter; it's blasphemous to find fault with a Good Game, or to search for redeeming qualities of a Bad Game.

Not every thing that stands in a forest is a tree, and not every detail of a Bad Game is terrible compared to those of a Good Game.