I saw this issue come up on the Apollo forums the other day. If you want to constrain the dimensions of an Apollo application window, use the maxSize and the minSize properties of NativeWindow. I usually do it in an initialization function after setting the bounds of my window, like this:
var win:NativeWindow = systemManager.stage.window;
win.width = 800;
win.height = 600;
win.maxSize = new Point(800, 600);
win.minSize = new Point(800, 600);
win.visible = true;
You can also use the bounds property of NativeWindow to set its size and location at the same time.