I have just bought some carbon look guards for petrol tank and exhaust for my bike and when fitting I realised the the bottom bolt (closest to footpeg) on either side tank/exhaust is different? The one on tank side has a nylon lock nut on the back of it where as the exhaust side just threads through the frame into some silver washer type thingy? Are they supposed to be like this or is one of them wrong?

Yea, the one on the muff is a vibration insulator of sorts. Has a rubber insert or something as I recall so things can shake just a bit on the muff side without breaking.