Let's say, hypothetically, that you go out for a longish run, and, again hypothetically, when you return home and go to the restroom your urine is dark, with blood in it. Your first thought might be, "Oh my! What is happening to me!" But relax; it may be runner's hematuria, which is not uncommon in runners. If you're running with an empty bladder, the jarring motion of running may rupture blood vessels in the bladder or kidneys. So be sure you're drinking plenty, and if it persists, see a doctor. In the meantime, enjoy your run!
Note: I'm no doctor. And I know nothing about your physical condition. I just read a few articles on the internet. Nothing in this post is meant to be the definitive word about anything happening to your body.