You are adding the same ball every time. You need to create a new ball each time.
Code:
//Classes
import com.greensock.*;
import flash.ui.Keyboard;
import flash.display.MovieClip;
import flash.events.MouseEvent;

//Variables
var max:Number = 580
var min:Number = 20
var timer:Timer = new Timer(1000, 5);

timer.addEventListener(TimerEvent.TIMER, onTimer, false, 0, true);
timer.start();

function onTimer(evt:TimerEvent):void {
  var ball:MovieClip = new Pelota ();
  var randomNumber:Number = Math.round(Math.random() * (max - min) + min);
  addChild(ball);
  ball.x = randomNumber
  TweenLite.to(ball, 3, {y:504});
  trace (timer);
}