Pretty common when you're new to such weight/volume overhead. In that sense, it's unavoidable initially. But it's important to recognize the difference between some break-in discomfort and pain arising from poor overhead positioning.
First, that overhead position needs to be solid - shoulder blades BACK together first, THEN up. If you drive up only, or the scapular retraction is weak, you're settting yourself up for shoulder pain.
Also, constantly failing to lock out jerks or snatches upon receipt can flare the ACs up. If this is you, spend some time really working on whatever technical issue is preventing you from getting proper lockout, and set you ego aside and lift according to your 1RMs with perfect lockouts (as you should be doing anyway).
Flexibility is obviously a big part of the deal as well. You may want to try subbing kipping pull-ups into the workouts some of the days it calls for deadhangs to really stretch out that shoulder girdle and get some connective tissue conditioning. Incidentally, that's why pull-ups are programmed so regularly - they make a huge difference in shoulder health.