Cshilt, when you first posted about this, I thought that the umpire told you it was "too late to do anything about it" because ANOTHER pitch had been thrown after the illegal pitch.
Do you mean that the pitch that was called illegal is the same pitch that was batted into the Fielder's Choice?
If that was the case, then there wouldn't be any reason for you, as the coach, to "get the umpire's attention" or "get play stopped"!
If an illegal pitch is batted into play, and ALL runners (including the batter-runner) do not safely advance at least one base, then the offensive team has the option of enforcing the illegal pitch penalty or accepting the results of the play.
If everybody advances one base, the illegal pitch is ignored.
So, let me see if I have this right: Pitcher does "something" that warrants an illegal pitch call, umpire sees and signals the illegal pitch, then the batter hits that SAME pitch, resulting in the Fielder's Choice...right?
Umpire could have- and should have!- called time at the end of the play and enforced the illegal pitch penalty. That can be enforced up until the NEXT pitch is thrown.
If I'm understanding this right, the umpire told you it was too late to enforce the penalty because the ILLEGAL PITCH had been thrown?
That is a total misinterpretation of the rules.