Batter's position in box

[bob jenkins]

If the batter starts partially (or entirely) outside the box -- fix it if you can. If you don't fix it, then there's no penalty for this action.

The penalty is only for hitting the ball with the foot entirely outside the box (or, in some codes, touching the plate). The batter didn't do that in your play, and so "no call" (well, just the strike) was the right call.