Everyone at some point or another will experience discomfort while playing guitar. It is pretty unavoidable as you are teaching your body to do something new in a position that really doesn't merit any other activity. First and foremost, you never want to experience extreme pain. If you do, STOP! No matter how long you have been playing don't over do it. Even for me as much as I play I still from time to time will experience discomfort and when that occurs, I am done for the day. Don't play through the pain. Take a break, and come back later as you will adjust to play comfortably. :)