Can different size feet be a cause of knee pain?
Foot size difference is unlikely to cause pain directly, but having an oversized shoe on the smaller foot may provide insufficient support or too much movement.  Try additional socks on the smaller foot, or an extra inner sole.

Given one foot is smaller, is it possible that leg is a bit short too?   You'd need to consult a sports physiologist, or possibly get a professional bike fit.   You can use longer bolts on your cleat, and some packing between the cleat and the shoe.

Finally, could it be a simple cleat mis-alignment?  I have recently gone clipless, and its shown me my left foot prefers a different position to my right foot.   Mind you my saddle always feels wrong unless the nose is 2-3 degrees to the left.