The Scene component is responsible for scaling the elements of the scene to the actual resolution of the device. So no matter the device, the scene along with its elements always fit the screen.
As far as I see it, you currently create a structure where multiple scenes are used.
(GameWindow -> Scene (GameScene) -> Loader (loads your level) -> MyGamegameScene (Scene within your level)
As both scenes try to scale their contents to match the device window, things get messed up at this point.
Just try to build your Levels in a way that doesn’t use an additional scene and you should be good to go. 😉