Wood is a natural product, and as it oxidizes and is exposed to light, it changes color. Some species-American cherry, Brazilian cherry and others, especially exotics-are known to change color drastically. There is no way to prevent this, although waiting as long as possible (ideally, at least six months) after the floor is installed to place rugs can help. So can moving area rugs from time to time. If you already have distinct lines on the floor, though, there isn’t usually a quick fix to remove them (even resanding won’t always remove the color difference).
The unexposed part of the floor will eventually “catch up” to the rest of the floor, if you can live with looking at the floor as-is until then.