Can low octane rated gas be the reason for 3 cylinders to constantly misfire?

Nope this is a fuel issue. Basically the car is made to run on the highest octane gas you can buy. Lower octane gas will foul out your spark plugs and cause other parts to misfire. My advice to you is to drive the car till the tank is almost bone dry then refill it with high octane gas after replacing the fuel filter and redoing the plugs again. Do not cheap out and use ngk plugs. Use the best Bosch plugs you can buy roughly costs about 89 $ for a full set. ONLY replace the plugs after you have all the old gas used up. Your car once its been driven a while after you have used up all the old gas and have the new high octane in it it should eventually even out and start running smooth again. And this is why you don't use regular gas in a vw or audi as it will only cost you more in the end then the gas is worth in savingings.

Oh and be sure to replace the fuel filter and then run the car for about 15km to make sure the old gas is fully out of the system before doing the plugs.

Thank you. I was just wondering why this only affected 3 cylinders and not the other 3?

i would assume it only affected one side of the engine right ? it may just seem to have only affected one side of the car but really it has affected all your plugs. The fuel does not fire correctly because the engine expects the best gas as its more refined. All vw and audi engines work the same and i think it also has something to do with there completely pressurized systems.