jackrae:
If your design is a true traffic light simulation there is a condition where you will have two LEDs on each column lit simultaneously. In the UK this is Red + Amber. The full sequence being Green -- Amber -- Red -- Red+Amber -- Green. The sequence may be different in other systems. I presume at the moment you have a current control resistor attached to each LED. IF, and it's a big if, a sequence group of 3 LEDs were controlled and lit singley then you could use one resistor to drive each LED in this group of 3. Each group of 3 would require their own current control resistor. Because you may have 2 LEDs operating together you cannot use a single resistor because the current demand of the 2 in parallel is obviously greater than the individual LEDs. Say each LED has a specific current demand (say 20ma) the current limiting resistor is sized to suit this current, generally somewhere around 180ohms. Two LEDs lit together will require 40mA or so and the voltage drop across a 180ohm resistor would exceed the output voltage of your arduino, or to put it another way the drive current through each LED would be approximately half of what it should be and the LEDs would be dimmed.
You're right, I do have red and amber lit up at the same time. Thank you very much.