Could be so many things, but with the limited info you've given it's impossible to give sound, structured advice.
Where specifically is your pain? Is it bench pressing or OH pressing that causes more problems? Push ups problematic as well? Do you participate in any other activities/sports besides just lifting? What there any specific injury that occurred or did the pain just come up after lifting? Any history of previous/old injuries to that shoulder? What benching technique do you use?