cloneEventsDeep: function(from, type){
	if (this.getChildren().length > 0) {
		this.getChildren().each(function(item, index) {
			item.cloneEventsDeep(from.getChildren()[index], type);
		});
		this.cloneEvents(from, type);
	} else {
		this.cloneEvents(from, type);
	}
	return this;
}

Put this snippet into the mootools core file right next to the cloneEvents function.

Mootools cloneEventsDeep clones events from children too

JavaScript