No pain, no gain
So, you are running. Then you know that old saying: no pain no gain. Somewhat true, you must push yourself over the limit, if you wish to achieve more. There are some minor nuisances which are not requiring any medical treatment, but can make your next run a hell. These are aches, blisters, and sore muscles.
Your body can't send you a written notice that describes in detail what bothers it. It will just ache in the problem area. Ache is an early warning system, and should not be taken lightly. Aches are normal, especially for beginners, but some of them indicate a more serious problem. If ache comes and goes, you can dismiss it, but if it persists, if it is there when you begin to run and it is still there when you are done, it might be an indicator of a strain injury.
If there is pain somewhere in your first mile, walk a bit. If the pain is still there, quit. If the pain in that location is there for days, go and visit a doctor. What you should do is ice the hurting spot to reduce inflammation and soothe the symptoms. You can also take an anti-inflammatory drug after the run. Is there something you can do to prevent aches? Of course. Remember to stretch regularly, and certainly before and after the run. Do not exert yourself, increase mileage gradually. Also, avoid too soft or too hard surfaces.
Blisters are results of chronic friction, and can go from nothing into raw nerve pain in minutes. If your feet slide even a little in your socks or shoes, you will end up with a blister. You can protect your skin on friction points with moleskin, duct tape, or medical tape. In the field, even a leaf can do the trick. Puncture blisters with a clean needle after the run and drain them (if they did not rupture by themselves) and protect them with band-aid or similar. Blisters are mostly results of inadequate shoes. Choose shoes that are a bit larger than you thing they should be.
Do your muscles feel stiff after exercise? Of course. There are two kinds of stiffness, good and bad. The good stiffness is caused by microscopic tears in the muscle tissue. This type of stiffness is both normal and necessary for getting into better shape. Then, there is the bad stiffness. This is a result of pushing yourself too hard for too long. Injuries in the tissue are worse, and you need to rest. How to tell the good from the bad? The good stiffness should pass after a day, while the bad stiffness worsens a day or two after the training. While this lasts (it takes a couple of days to recover), do not run, as you will worsen the injury and risk to damage other tissues as well, not just muscles.
If you must exercise, try something low-impact, like cycling or swimming. Ice the sore area, and try massage. Once you are back on track, take it easy, and if soreness does not wear off within minutes, quit. Wait until all traces of of soreness are gone. Best prevention of bad kind of soreness is gradual increase in mileage and "bursts".