When you exercise, be it impact or not, you build up lactic acid in your muscles. Stretching would be better used after you have cycled to try and help the removal of lactic acid. The thing to avoid would be a hot bath as well when you get home as this may exacerbate things.

The other thing is that perhaps you have increased your mileage too quickly. If the stretching doesn't help, then reduce your milage again and gradually build up. I definately wouldn't advise increasing your milage at the moment as you would just get worse.