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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).

Think the problem here is, that maybe your controllers imitating the keyboard and therefore you have some odd configurations. I personally had the same issue with my steam controller, i had to change the settings in the config panel of the steam controller menu. Don't know if you have something like that for Logitech.

The logic how players join and get there colors will change in the future, maybe the system is much more solid after that but unfortunately that is not something for the near future. :(