Thanks for the questions, guys. I'll answer as many as I can.
When Lugo stepped out of the box in the third inning (eventually grounding out to second base, it came under rule 6.02 (b).
"The batter shall not leave his position in the batter's box after the pitcher comes to Set Position, or starts his windup.
"PENALTY: If the pitcher pitches, the umpire shall call 'Ball' or 'Strike,' as the case may be."