Stolen base?

This happened in a 12U travel game last night. Runner on 1st. Pitch is delivered and caught by the catcher. A ball is called, it is ball 3 but batter thinks it is ball 4 and starts to 1st. R1 starts moving to second when he sees batter heading to first (he did not attempt to steal on the pitch). Ump calls batter back, but the batter kind of stops for a couple of seconds like he is questioning the call. In the mean time R1 stops moving to 2nd when he sees the batter talking with the ump, just stands about 1/2 way to second. Then the base coach tells him to run to second as it is a live ball. Ump says R1 has to come back to 1st. No one, including ump, called time out. Was placing R1 back on 1st the right call? Seems like the correct call to me (but of course my son's team was in the field ) I am guessing this is not the first time this has happened, so I made a mental note to ask the experts here. Thanks in advance.