Correct batter is on base??

[kfo9494]

One of our high schools had an intersquad game Sat and invited umpires to call the game. This is a good situation to see new umpires and get ready for the season.
This is VERY informal but the coach wanted a game feel to the practice and divided the team up with each having a coach, line-up and score.
I will try to explain this situation the best I can--
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In the 5th inning the blue team came in to bat. The coach of the blue team wanted to make a few subs and gave them to the umpire and the other coach.
S1 was going in for B1, S2 for B3. He told the umpire behind the plate and the other scorer.
However!- S2 batted for B1 got on base, B2 struck out, S1 comes up to bat.
After three pitches (2-1)the white coach came and said they are batting out of order. The correct batter is S2 who is on first base.
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As I was watching my head was swimming with "What the hey!"
It was so informal the blue coach just yelled that he got them confused and it was changed with no more interest.
I meant to ask but other things happened and I lost track of the question.
What is the correct procedure for this situation?