When using this template,any new document added is always formatted as New Scene, whereas outside of the script, I think the default is supposed to be New Text.
The way Scrivener works is this: whatever item was last selected when you make a new one will determine if it is script or normal. So that would explain why you typically see script files inside the Draft folder (since the template starts you out with one there) and normal files outside. Whatever the case, it is easy to switch types if you make a mistake. Just hit Cmd-8 to toggle the type.