Base on Balls Bases Loaded

[For the kids]

Bases Loaded and Batter receives a base on balls. Umpire--who is behind pitcher on the mound--calls runner from third out for not touching home plate which if she did miss it not by much. Anyway the question is: Where in the rulebook does it say that this is the umpire's call and not up to the defensive team to appeal a missed base? Also where is the rule book does it negate section 5 rule which states: Base runners are entitled to advance without liabitlity to be put out: A:When forced to vacate a base because the batter was awarded a base on balls? We had this situation where the umpire called the girl out without the defensive team appealing. This was an ISA umpire who made the call--I have always believed that in a missed base situation it was up to the defense to appeal the play and is it different on a base on balls where the ball is in the pitchers circle and there was no play being made. Even though it was ISA I would appreciate any/all feedback on this situation. Thanks.