So sorry for ignoring this for so long. Muscle tissue is layered; it folds on top of itself. If one layer is damaged and repaired, this could result in scar tissue (which should subside over time, but may never completely disappear). So what is probably happening is that there is a "bump" in one layer of your muscle, where before there was not, and the layer either on top or below the damaged layer is catching on it while it moves. While it may not be normal, it's also not very detrimental, unless it accumulates. So take just a little extra care with any area you have ever injured, and a lot of extra care of the areas you have injured repeatedly.
As for the hips and shoulders, that's usually a result of the same sort of aforementioned phenomena. The difference is it's usually a result of muscle catching on cartilage or bone. That's normal in all joints, especially those surrounded with large amounts of muscle (hips and shoulders, not so much toes or fingers). That's not so normal where there are no joints, like the gracilis muscle, which connects your pubic bone to your tibia (suspected discomfort perpetrator).
Hope this helps. Take care of yourself.