I remember the moment when it suddenly struck me that not every short muscle is a tight muscle. I can't give you an exact date and time, it wasn't quite that sort of epiphany, but it was a jump in my understanding of soft tissues and how to treat them.
I was reminded of this today when I came across a short article over at Kinetic Revolution looking at the issue of tight hamstrings when the real cause lies the position of the pelvis. An anteriorly tilted pelvis can make the hamstrings feel tight when in fact the issue possibly lies with the flexors pulling the pelvis forward and lengthening the hamstrings.
Treating the hamstrings as tight could lead you to think that they need stretching, but that only exacerbates the actual tightness in the flexors. Release the flexors and the hamstrings will sort themselves out in all probability.
The implication here is that when you test the hamstrings, then you should be looking at the pelvis not just at how far the client can bring the hip into flexion with a straight leg. And of course you should also test the hip flexors.