Many aches and pains in our body come from muscle imbalances. Make sure to stretch your body evenly, right vs. left, and front vs. back (e.g. quads vs. hamstring). Even if you have pain in only one side, you should always stretch both sides.
When performing a stretch, proper position and good posture help relieve tightness and increase overall mobility while minimizing injuries. Move as deeply into each stretch as possible before reaching a point of discomfort. Stretching should create tension during the stretches, and relief afterwards.