Any time you engage in physical activity beyond what you are used to, you will have some aches and pains. Given proper rest and nutrition, with continued training your aches and pains will become less and less, or at least it will take more and more exercise to elicit them. I will guarantee that even the top pros get sore after hard training or competition.

Consider some kind of conditioning/cross training to address specific concerns. Pilates, yoga, stretching, core exercises, foam rollers or balls, all have their place in reducing discomfort on the bike. If problems continue or worsen, a trip to a sports oriented physician or physiologist may be in order.