I am often asked what it means when a knee makes noise during an exercise routine. If the person asking the question is exercising under my immediate guidance, I tell him or her to stop the exercise. Then, if no pain reduce the resistance, check for proper mechanics and restart the exercise and monitor at a lower intensity for a set.
If there is pain, then it is time to stop that portion of the workout and depending on the level of pain, the person's health history and reason for having a workout, we would decide the next step. Typically, my clients come to me already with some kind of knee pain, usually knee osteoarthritis, and are or have been under the care of an MD or PT and the goal for seeing me is to create a strengthening program that does not cause pain or additional injury.....As a caveat, with any new, exercise related, joint pain, it is always best to consult your MD.
If you click on the link below, Kevin Stone, MD answers this question in much more detail.