What you’re seeing isn’t a bug, but just the way scene trees work in Godot.
Each scene can only have one base node. Every node you add to that will be a child of that, or a child of one of those children.
Player is the root node of your scene and you can’t have multiple root nodes. If you want a different parent for your 2nd sprite create another root node and put Player and the 2nd sprite as children to that node.
If you don’t want a sprite to be apart of your current scene, You’ll need to make another scene. If you want them to interact, you’ll need to have another scene, (AKA a level/world scene). And instance the other 2 scenes in. In short you’ll be needing 3 scenes total.
world
–player (instanced in)
–otherthing (instanced in)
to instance in a scene click on the chainlink icon (it’s right next to the plus symbol(the one that adds nodes into your scene))
It’s how Godot’s node system works. It’s a good idea to look at the Godot Documentation when your stuck.