Personally, I would agree that if the 12th player is sprinting off the field, is outside the numbers and *might* not make it, you let that go and make it a live ball substitution foul if he doesn't make it.
However, if he's still got to cover half the field and will definitely be influencing the play after the snap on his way off the field, you should shut that down pre-snap for a 5 yard foul instead of a 15 yard foul. You can also tell when the snap is imminent by knowing the general offensive cadence and/or watching the play clock, especially later in the game when you're familiar with their play calling.