Hindsight is indeed 20/20. Unfortunately, your story is more common than people (especially the young or those new to training) want to believe. In fact, it almost reads like a text book example on how to injure the shoulders benching.
I agree with dels322. Get the area examined so you know exactly what's going on.
A full range of motion is NO guarantee that you are not injured. The fact that there is pain when you hold resistance is a loud and clear sign of possible pathology (in fact, many people have zero pain and still have issues with shoulders, spine, etc.).
The worst mistake people make is to train through the pain because it always feels better after a few warm up sets. This is a horrendous way to think - unless you're one those idiots who love to brag about his surgical history as if it's a badge of honor.