There are a couple of factors which may cause a joint pain in exercises. But even more important is what you do about it.
First of all, there is the nutrition factor to be considered. My top recommendation is Fish Oil. Another great one is Turmeric, which is a great anti-inflammatory. There are many others things you can do to lessen or prevent joint inflammation, but once your nutrition is in good order your body will be able to heal itself.
The second component is all about the way you exercise. That means proper form, since bad form is one of the causes of joint pain. However, some things are individual and depends on the way your body is built. There are some great exercises in general, which just might not be the best for your body and joints. So you should do some testing and figure out what works best for your body.
Moreover, you want to make sure that you get to lockout in exercises like kettlebell overhead press. Getting into the locked out portion, contrary to what is recommended in bodybuilding, will help strengthen the joint.
The last thing regarding joint pain is to take care of the volume and the intensity. If you experience pain in your joints, that weight is probably too much for your body to handle at that particular moment or your sets and reps need to be tuned down. Joint pain in exercises can often be from over-use. Often times less can be more.
Many people will find bodyweight exercises are less harsh on their joints then weights. That doesn’t mean weights hurt you and bodyweight exercises don’t. Far from it. Everything else still applies it’s just that even in exercises you’re handling your full weight its often less than what you’d handle with weights.