Current practices in medicine?

I read this article last night, from the NY Times Sunday Magazine: Shaken-Baby Syndrome Faces New Questions in Court. It reminded me of a case I had breezed by when I spent my time shadowing at a children's hospital. The resident mentioned retinal hemmorhaging, and I asked what that meant; he responded once out of earshot of the that it was most likely caused by someone who had shaken the baby violently enough to cause blood vessels to burst in the retinas. I didn't get to follow the case after that conversation; there were other patients to see. But, this article made me wonder-- was there a guilty family member? friend? or was it really just caused by some sort of infection? I've wondered about what sort of protocols are currently in place in the medical field that may be based upon incomplete findings-- in essence, we're not seeing the whole picture.