The only time my shoulders get injured is when people try to "fix" my chaturanga. It is always the ones who feel that your arms should be at a 45 degree angle, elbows over wrist, shoulders come forward and that you should only go down but so far. This does not work for my body. It does for others. As an Ashtanga practitioner, I can do hundreds of chaturangas a week with no problem but the minute someone starts trying to fix my alignment(how far I lower and my elbow and shoulder placement), pain comes.
If you look at videos of yogis who can do amazing arm balances and float in and out of poses like leaves in the wind, many of them don't have the "perfect" chaturanga and to say that they are not strong would be to deny reality.
When I work with my students on chaturanga, I focus on what is going on with their core and their scapula. I look for stability when they lower. For most people,once they get strong in the core and the seratus is stable, the shoulders and elbows work themselves out.
It is important to remember that we don't do yoga for the sake of doing yoga. Meaning, unlike the olympics, someone is not judging our form and its perfection. Yoga is about making our everyday life better. If doing "perfect" alignment jacks up my shoulders, how is that making my life better? I have been practicing for about 11 or so years. I think that is long enough for me to know that what I am doing with my chaturanga is not causing me any harm. Here is a great video on it.