Al,
I realize this is only T-Ball but it's always a good time to educate the coaches on the rules of the game.
As for having two players on a base at the same time while the ball is live. This is perfectly legal. As long as the following runner does not physically pass the preceeding runner, there is no violation. The defense must tag the runner who is not entitled to the base to record an out. Nothing is automatic.
Now, which runner is entitled to the base?
The preceeding runner is entitled to the base unless he/she is forced to advance. In your situation, the runner coming from 2nd base on the original play (the preceeding runner) is entitled to the base because she is not forced to advance any further than third base. If the following runner advanced to third and the ball was still live, the defense would have to tag her to record the out.
All of this is moot in your situation since you had called "time".
Ain't T-ball fun??