Because the films are nonsense.
I'm sorry, but that's the long and the short of it. In the books, Harry and Lily both have green eyes. In the films, Daniel Radcliffe (playing Harry) has blue eyes.
This problem was actually considered by Rowling and others while the films were being made:
Rowling: Sometimes I’d dig my heels in about the funniest things. I’d say, “Yeah change the costume. Yeah it can happen in that city instead of that city. And all of a sudden, I’d say, ‘But they wouldn’t do that spell. Why would they do that there? So I think sometimes I confused people. But I also remember, right back at the beginning when you were cast I remember David Heyman calling me up and saying, “We’ve tried green contact lenses. We can digitally alter his eye color in post production. How important is it that his eyes are green?”
Radcliffe: That I will thank you for.
Rowling: And I said, um, “The only really important thing is that his eyes look like his mother’s eyes. So if you’re casting Lily, there needs to be a resemblance, but they don’t absolutely have to be green.” “Oh thank Christ,” he said.