Thanks for sharing the project, it was very easy to find the problem looking at it:
You have in your
Concept scene a
Sprite as root node and it has a script which is blank.
All scripts have to have an inheritance (the
extends ... part). It can be another script (put the path of the script, like
extend "res://myscript.gd") or an object (
If you don't have an inheritance at all or it's wrong (if you had, for example, a script in a
Sprite node that extended an
Area2D), it will not run and return this error.
It was not very explicit in the error message since it had no inheritance at all (this is why it was saying "inherits from native type 'Reference'". If you had, for example,
extends Area2D in that script, the error would be "Script inherits from native type 'Area2D', so it can't be instanced in object of type: 'Sprite'".
To solve that you can or delete the script since it has no code or add
extends Sprite if you plan using this script in the future.