Comp, in your opinion or the rulebook's, shouldn't the umpire always draw attention to the fact that it's only 3 like you did? It sure would save the hassle of trying to deal with the complaints afterward.
Also, WHAT IF you had made a mistake and either called ball four or told her to take her base only to find it was ball three? Would you send all the runners back?
It seems easy to correct and it seems like the defense shouldn't be punished for the mistake of the umpire.
Answered in post #13.