 The original plan was to have the circuit lines of the "good"  programs glow yellow, and the "bad" programs would have blue circuit  lines. At one point this was changed to where good programs are  blue, and evil ones are red. Some of the original coloring remains,  mostly in tank programs (Clu has yellow lines on his uniform, and  all of Sarks tank commanders are pale green).But Flynn takes on  this greenish tint after he crashes the reconizer and gets knocked  out, shortly after he gets up he returns to the normal blue.