Foot Problems

Recently I’ve started training for a half marathon.
After my long runs (I’ve only done 2 so far) I’ve noticed a painful bruise on my foot.
The pain is like a bruise but they look at feel like a small stone in my foot. (not on the bottom of my foot, but on the side)The first one is on the outside of my left foot.
It was painful at first to touch but now (it’s been over a week) it doesn’t hurt anymore.
The second one came only about 2 days ago.
It is on my right heel and feels/looks the same.
They don’t hurt when I’m running, even on my long runs when (I assume) they develop.
I’ve been a runner for 9 years now and I’ve never had this problem.
What could it be?