Well if one parent had blue eyes, and the other had brown. That does not mean that the child would have blue-brown eyes. Now I am not an expert in genetics (my experience mostly consists of short lessons in biology and chemistry classes), so I do not know much, but Arwen would not have to have blonde hairs in her hair. And I also think that we have to also consider that elves are kind of special, and Arwen was specifically a very special elf. So I think her hair color was on purpose in a way.
Am I making sense?