Not sure if bug, or just user error.

Main.as

package
{

  import ash.core.Engine;
  import ash.core.Entity;

  import flash.display.Sprite;

  public class Main extends Sprite
  {
    public function Main()
    {
      var engine:Engine = new Engine();
      var a:Entity = new Entity("a");
      var b:Entity = new Entity("b");
      var c:Entity = new Entity("c");
      var d:Entity = new Entity("d");

      engine.addEntity(a);
      engine.addEntity(b);
      engine.addEntity(c);
      printEntities(engine.entities, "Starting list");

      engine.removeEntity(b);
      printEntities(engine.entities, "Removed b");

      engine.addEntity(d);
      printEntities(engine.entities, "Added d");

      engine.removeEntity(c);
      printEntities(engine.entities, "Removed c");

      engine.removeEntity(b);
      printEntities(engine.entities, "Removed b again");
    }

    private function printEntities(entities:Vector.<Entity>, message:String):void
    {
      var names:Array = [];
      for (var i:int = 0; i < entities.length; i++)
      {
        var entity:Entity = entities[i];
        names.push(entity.name);
      }
      trace("LIST: " + names.join(", ") + " (" + message + ")");
    }
  }
}

trace.txt

[trace] LIST: a, b, c (Starting list)
[trace] LIST: a, c (Removed b)
[trace] LIST: a, c, d (Added d)
[trace] LIST: a, d (Removed c)
[trace] LIST: a, c, d (Removed b again)