Having a similar issue to the one reported a year ago...
Windows 10 machine, 2 Xbox-compatible controllers (Logitech Dual Action).
Player 1 joins (Top-left). Top-left appears correctly, but so does the bottom-right character. Same thing happens when Player 2 joins first.
Player 2 joins, and we also get Top-right.
Once both players ready up, either player can hit A again to also ready up the extra character. When the game starts, BOTH controllers ALSO control the third character, which I'm guessing is the keyboard/mouse player (Even when no one is using that).