I have the smae problem - kicking my left ankle, which makes it bleed.
I tend to be a bit of an on-off runner, and generally find it a problem when I restart running (have a scab right now!). It seems to be that I "flick" my foot as I run. Once I get stronger, I just seem to run more smoothly and I don't seem to do it. Either that or the skin toughens up, though I don't think it's that.
Some trainers are wider than others, so if you've changed shoes recently that may explain it, or some off roaders seem to have sticky out bits there to increase grip.