1. Was I stretching what I really thought I was stretching? Probably not. A great example is the hamstring stretch I see everyone doing (similar to the diagram). What are you actually stretching? Well, you might be stretching hamstring, but you are also stretching the joint capsules and ligaments in your low back (this is a bad thing!) and the knee. You are also stretching the tendons that attach to the muscle and more importantly, you are probably stretching THE SCIATIC NERVE! If in fact you are stretching the nerve, it will cause the nerve to depolarize which will cause the muscle to contract! If your goal is to increase ROM, then you may have done the opposite and decreased your ROM. 
If in fact you can stretch the hamstring muscle (there are ways to do it properly), the muscle belly itself (the most elastic part of the muscle) only stretches to about 10% of its length. Thus, if the hamstring muscle belly is 40cm long, only 4cm of stretch comes from the muscle belly! So, then why do you actually reach further when you are stretching? There is a fair bit of research that shows that the apparent increase in ROM of a stretch is not necessarily due to the muscle length, but rather an increased tolerance to bear the pain of the stretch.
So I get asked...should I continue to stretch? My answer to that is that if you like to stretch, go ahead and continue to stretch (but you should get shown how to stretch safely). If you do not like to stretch, current signs show that it may not benefit you as much as you may think.
Dr. Mark Malowney is a Chiropractor, kinesiologist and Certified Strength and Conditioning Specialist located in Victoria, B.C. Canada. Please see www.drmchiro.com for contact information
