After doing some research with multiple people, they say that limited slow exercise to harder work outs are better, and then to stretch once you are done, as your muscles are now ready for the stretch. The problems that can occur while stretching while the muscles are still cold is what LBB mentioned. You can actually hurt yourself stretching before the exercise. I think a lot of that has to do with improper stretching techniques also.
Remember to stretch slowly and do not bounce. Hold the stretches and extend them out a little farther, but only do them slowly.
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2007 Jamis Ventura Comp
2006 Jamis Explorer 2.0
2000 Specialized Hardrock (bought used)
Swim, Bike, Run and sounds like fun