Happens to me too. Just as you say, kick the inside of my ankles. No scabs, but if I wear socks it's obvious from the dirt marks when I do it. Also, it happens the most on long runs... probably when fatigue sets in?
I know I have some form/strength imbalances. A bit of anterior pelvic tilt, hips rotate to the left a little, and my right glute is noticably weaker than the left (shows up during single-leg squats).
I don't know the cause. I would like to get my strength imbalances resolved at some point. I have a feeling they are all tied together.
I wear both stability and neutral trainers.