As far as I can tell there's no problem here, it's just your events are wrong.
If you say "Spawn bullet on layer 0" (providing a number to identify the layer), then add a new layer which you set to the bottom, that is now layer 0 (see the numbers to the right of the layers bar, those are the layer indices). If you give layer number 0 a different name, like "Layer 2", you will just confuse yourself - it's layer number 0!
Also note carefully each layer's transparent setting - you're putting a transparent layer beneath a non-transparent layer, which means you'll never be able to see the bottom layer.
Refer to layers by name instead of number and you'll always get the same layer no matter where you move it.
If you're still sure there's a bug, try making a new .capx from scratch. As it is it just looks like your project is set up wrong.