For a little more context, I use an 8bitdo Ultimate Wireless controller. The one that works on the Switch, PC, and the Deck, with my Deck docked to a TV while playing for this to happen. Haven't tried to recreate the issue undocked, because I don't use the Nintendo layout undocked.
I've had a few games where I press a face button (ex. The A button), it acts like I press the correct button for a second, but then immediately after it presses the Xbox counterpart. Like, when I press A, it presses B right after, which makes it really hard to navigate menus.
The layout works well with most games I've tried, but I've had these issues in Cyberpunk 2077 and 30XX.
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Your suggestion worked! Never knew you could disable Steam Input… Thank you so much!