That kind of bugs me too. They make such a big deal about how green and beautiful is eyes are in the book and yet completely change the color for the movies. They might not have thought about it in the first movie so never changed it. Also his eyes are gorgeous as they are and they might not want to cover that up. mostly I just don't think the director and costume designer thought changing his eye color was that big of a deal...they don't always follow the story line that closely anyway --- I hate that they keep giving Dobby's parts to Neville---.
He might not be able to. Some people can't wear eye contacts because of their sensitivity to them, so they left that out. On the other point, he might not have WANTED to. I hear contacts can be uncomfortable, especially theatrical ones.