They are executing certain things in certain ways or implementation of how Nintendo implemented it was the only thing Nintendo had patented.
Like the D-Pad.
they couldn't stop others from using d-pads, but they couldn't be shaped like Nintendo's.
you will notice Sony has the separated d-pad and MS has the rounded one.
with the joystick, Nintendo has the octagonal ring around it. Sony's is smooth and loose and I don't remember the difference for MS's, but I'm sure it's not identical to Sony's or Nintendo's.
BUt I think Nitnendo's problem was only patenting specific implementation instead of blanket patenting an idea, but that may be because they weren't the first ones to come up with the tech, just the first one to use it in the way that they are.