If you change the default key assignements (joypad), if you go in a minecart, the keys are still the default key assignement,
Device: GPD XD
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is duplicated by 4
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Not sure if this is exactly the same issue, but something doesn't seem quite right when you reassign controller buttons.
In my case, I found that assigning Jump to 'B' (button 2) worked, but if I then pressed 'A' (button 1) while in a cart, it would make me jump repeatedly.