When drawing shapes make sure the shapes are in the propers order.

In this example if the // face rect is drawn after the // mouth rect(), the mouth will not display.

This isn't working, it might not matter when not using the khan canvas interface
switch order
//Face
ctx.rect(faceX,faceY,faceWidth,faceHeight)

//Eyes
ctx.rect(eyeLeftX, eyeLeftY, eyeWidth, eyeHeight)
ctx.rect(eyeLeftX + (faceWidth * .45), eyeLeftY, eyeWidth, eyeHeight)

//Mouth
ctx.rect(eyeLeftX + (faceWidth * .125), eyeLeftY + (faceHeight * .45), eyeWidth + (faceWidth * .2), eyeHeight)