Hector's father goes to Achilles to ask for Hectors body back, to give him a proper ceremony and says he has to place two gold coins for the boatman (on his eyes, as seen previously on other dead soldiers). However as Hectors funeral pyre is lit at the ceremony he can be clearly seen without the GOLD COINS!!!!
I have Troy on DVD and have watched this part many times. I'm afraid to say you are completely mistaken. Although the coins may be difficult to see, they are, without a doubt, on his eyes.