Think about it this way... If you flew until the tank was empty, the fuel would go through your engine, so why not put it back in the jug?

But I don't know the reason why it's changing color. Like Mike Ledbetter, I always pump any remaining fuel back into the jug, and I think it's the most common practice. On the other hand, my fuel does not discolor. The 2nd most common practice is leaving it in the plane, but you risk the alcohol evaporating leaving fuel with very high oil content!