Misaligned cleats are a different issue. The misalignment imparts a torque on the joints up the leg in a 1:1 ratio.

On the other hand, a properly aligned cleat that is 1mm out of place causes the joints to be very slightly more bent or less bent (but still in the proper plane). And because of the distance involved, a 1mm change at the foot translates to thousandths of a mm at the knee and hip.