You can only see this at the part where you just start the level. Wait until Rtas 'Vadum and the other Special Operations Elites engage their camouflage, then look at his eyes. Although he's invisible, his eyes are still green and stand out from his Active Camo. This does not affect him in any way and does not occur with any other Elites.
It cannot be seen in Halo 3 as he can only be seen in cinematics and not in actual gameplay. This glitch also occurs with the Arbiter when viewed in Co-op, as his yellow eyes are also visible when his camouflage is activated.