Correctable??

[tarheelcoach]

I coach school ball - and I'm a relatively inexperienced umpire, so please provide me with the benefit of your experience.
Today in our first game, we had a situation where with two outs and a runner on third, the count went to 1-2. The next pitch was a called strike three - end of inning, right? No, the home plate umpire called the batter back and said the count was 2-2. I figured I missed a call earlier, and told my player to jump back in there. Of course, next pitch he lines the ball to the gap and ties up the game. The opposing coach then comes out to complain that it was strike three.
The umps get together, and they come out of conference to say that since another pitch had been thrown, it was too late to change anything (never saying whether the other coach was right or not, but you can guess.)
We went on to score two more runs in that inning, and won the game by 2, so the other coach was REALLY unhappy.

Could the umpires have taken away the hit and ended the inning if they realized it was strike three earlier? They never checked the book, but that was being done by a couple of kids, so they weren't a good resource.

BTW - neither umpire had a indicator!