Pardon my grammar, I'm using my phone to respond.
The kidneys are the hardest hit organ (besides the skin) when doing exercises. With the release of lactic acid, suppliment residue (if you take any), [Im]proper hydration prior to exercise, and just the everyday functions, somthing is bound to happen.
After my heavy weight training, sometimes my urine us darker than normal, or even a little cloudy; I check with my doctor (who specializes in sports medicine) and he said that its totally fine if there is some blood [just like a boxer urinating blood after a kidney shot]. But just like Paulflexes mentioned, just be lucky that there wasn't blood BEFORE your work out.
This may sound funny, or 'gross' or whatever, but moniter what comes out of your body JUST as much as you monitor what goes in. If you notice something in your urine or feces [or even if your sweat smells a certain way], your body not may be correctly responding to something and it may be serious.
Get your urine checked by your dotor if you haven't done so if this blood in the urine happens often.