Sorry nobody's really responded to your question. I'm not really sure what he meant by that, but as far as I know, brown spots in the eyes are normal. I have blue eyes, but I also have some brown freckles in them. My mom has them. A good friend of mine has them. And another friend of mine has an eye that is half blue/half brown. I'm not sure what it could mean genetically. But if you think about it in an evolutionary way, we all originated from africa, so it would make sense that some traits could be crossed over "racial borders," so to speak. I don't think that he's saying that you're great grandmother was african-american, though she might have been and there's certainly nothing wrong with that. I think it was just an observation. I wouldn't get too freaked out about it.
By the way, try to have your eyes checked more often. Some eye problems tend to escalate with age, such as far-sightedness. Plus, as you get older, your risks increase for cataracts, glaucoma, and, depending on your medical history, macular degeneration. Getting routine eye exams could really make some things easier in the future!
Hope this helped!