I'm not sure if the color at the stems are a true problem, many peppers do have color variation along stem.  This isn't enough information to make a diagnosis or be able to give you an answer to save them.   Please bring in a sample and we can try to identify and send you recommendations.

Our offices are located at 2001 South State, Rm #S1200, Salt Lake City, UT.  Directions to our office can be found on our website at http://extension.usu.edu/saltlake/htm/directions , we also hold Ask A Master Gardener clinics on Mondays from 1 to 4pm where we have both staff and Master Gardeners ready to answer your plant problem questions.

If you can't bring in a sample, a digital photo of the problem can be sent to me, to help you figure this out.