Sounds like you have a weakness somewhere along your kinetic chain so that when fatigue sets in your form begins to falter. My suggestion is that you work on exercises that create stability especially your glutes (bum). The crazy deal with running is that the cause of the issue is many times far removed from what you are experiencing. When you have weak glutes you can't stabilize your foot in the stance phase very well. This is done by working on your glutes as well as teaching yourself to fire them when running. But also note that you may need to work on hip extension exercises as well since this too can be an issue.
There is a really great book that you can get at Amazon.com for under $15 (here in the States) including S&H that I believe is going to become the runner's best friend in helping with injury prevention and running economy. The book title Anatomy for Runners by Jay Dicharry. It has helped me understand many of the issues I have experienced or am currently experiencing as an almost 7 year runner.
Could be, for lack of a better term "lazy feet". Just try to pay a little more attention to your jogging form. So when you do feel your foot hit your ankle, that tells you that you've taken your concentration off of your form. Happens to the best of it, hurts like a mother sometimes. lol
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I have been running for a year. About two months ago I noticed that sometimes when I run, my right foot hits my left ankle. It doesn't happen all the time and it is always the left ankle. Anybody have any idea what may be causing this and what should I do to try to stop?
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