From a quick Google search, it seems that the Unity Input System (which is the system the game uses to handle player input) tends to struggle with Switch Pro controllers on Windows and Mac, sometimes reading a single press from A / B / X / Y as a continuous press on all of them, and sometimes just registering random inputs.
This is most likely something we can't solve ourselves, this is most likely an issue for Unity and their team to solve since they know the system inside and out, and any changes we might try to make to the system could cause issues.
What I might suggest is trying to connect the controller via Bluetooth rather than using USB, if you haven't already tried to do so. That seemingly works better sometimes, but not guaranteed.
Thanks again for pointing this out to us! This will now be listed as a known issue in our changelogs and we'll keep track of this issue and let everyone know once it has seemingly been solved. 😁