Lisa:  Thanks for your question.  It would have been helpful to have a picture of your pepper plants, as coloration on plants can be caused by a number of factors.  However, assuming the plants otherwise looks healthy, and the dark areas are not sunken or wrinkled, it may just be a normal condition of the plant.  I have attached a picture of a typical case for you to compare.  The same may hold true for the tomatoes.  The fruit should develop normally and there is nothing you need to do.  If your plants don't look like the picture, then please send pictures of both the peppers and the tomatoes for an evaluation and let me know if you have any questions.