Red oak is pretty "grainy" so the dark brown and gray streaks sound about right. Is it possible your floor is "white oak", which is less grainy and more consistent in color? Or was your original flooring maybe stained that honey color or was it finished "natural"? Wood, being a natural product, is going to have differences and inconsistencies even though it may be the same #1 red oak. Also, hardwood floors change color over time (exposure to sun, etc) and so your original floors may look nothing like #1 red oak anymore, even though that's what it is. Lacing in new wood floors with old is always tricky. You might want to consider refinishing and staining the whole floor to one color. Other than that, I would imagine you'll have to fight it out with your contractor. Have you shown him the floor in it's current state? What does he say about it? If he's a good contractor, he should be able to work with you to come up with a solution. If you're not happy with his work, he'll lose you as a customer and as a good reference, so it's in his best interest to make sure you're satisfied. Good Luck!