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You are probably weak. You need strength training and stretching. It's all very well developing your muscles by running, but it takes longer to refine your tendons and ligaments. You also need to assess your running technique - i.e. where are you putting adverse strain on your body and how to correct this? Many athletes require a trainer to hone in on developing their self awareness of body position in space (proprioception). Also, equipment has to be right for you, shoes fit and give appropriate support for your distance. Not forgetting diet, hydration and stretch recovery.
Sounds crazy but ballerina exercises are amazing for strengthening ankles. Standing on tip toes on one foot for as long as you can until your ankle is strong enough not to wobble while supporting your whole weight. Also, horse riding is great for stretching achilles - get those heels down while strengthening your knee ligaments through the fixation of your thigh and lower leg against the horse which in turn gives you incredibly strong muscles and excellent balance.
Difficult to advise specicifically as you've not mentioned where you're getting your injuries. Try to make sure when you run, your stride flows as a continunous motion from one stride to the next to prevent any jarring. This again may require input from a trainer. There is nothing like a trained eye who can offer you the smallest bit of advice that makes the biggest difference.