Just in case anyone might think that the umpire was "making stuff up", this is an actual rule on the books and the penalty is indeed an illegal pitch call. Personally, I can remember calling this only a couple of times in a span of hundreds of games.
If it's borderline, instead of saying anything to the pitcher I will talk to her coach about it. My feeling is that telling the pitcher how or where to step borders on coaching, and umpires are lectured to never coach a player. The coach can then use this information as he sees fit, and consider it as a warning- even though it's not officially a warning, as the rules do not instruct an umpire to give a warning for this infraction.
If it's blatant, I would have to call it right away. I would also be more likely to call it if it happened after having had a talk with the coach about it.
In a single umpire game, this is one of those calls that is almost impossible to make unless it is blatantly obvious. As the plate umpire your priority is the ball/strike call. With a 60 mph pitch reaching the plate in about four-tenths of a second, your focus has to be on the strike zone.
In a two umpire game, the base umpire is more likely to make any illegal pitch calls involving the pitcher's foot placement.
On a side note, in the men's game this was so prevelent that the requirement to step within the width of the PP has been lifted, much the same as the rule against leaping was lifted for the men several years ago.