Stair thread different color from old runner carpet
What you're actually seeing is the polyurethane that's been exposed has ambered ( turned yellowish ). Sadly, that's a byproduct of using oil based polyurethane. Now that the center is exposed it will eventually amber as well.

If it really bothers you, you could try sanding the treads just enough to remove the existing finish. Just be careful not to sand thru the stain. Then clean the treads, with a rag lightly dampened with water or paint thinner, to remove any dust left behind. Finally recoat with fresh polyurethane. I'd recommend at least 3 coats with a light sanding in-between each coat to remove any bumps or bubbles and to give the next coat something to grab and stick to.