Left shoulder joint and knee pain.

I have lately started working out in the gym but nowadays I have started getting joint pains during and post workout especially in the knee and left shoulder. Also can hear some crunching sound in these areas if I move or bend them normally without weights. Is this something serious to worry or is it because I have started working out? My gym instructor suggested me to consume the capsules with Glucosamine, chondroitin and MSM for a month or two to get relief and strengthen the joints. But is it safe to consume those supplements? I used to get knee pain even before whenever I used to jog or bicycle longer distance, but the shoulder joint pain has started recently after working out in the gym. Also I do get neck pain frequently. Please assist or advice.