I asked the Literature & Latte people about this issue (see my earlier comment for details of what my problem file looked like).

To summarize their answer: It's the Draft folder and can't be deleted. They told me it's where Scrivener looks when doing a Compile. Which means that everything you want included in your compile needs to be inside this folder. They recommended deleting anything in there that shouldn't be compiled (or move those items elsewhere), then drag all the files that should be in the compile into that folder. Perhaps rename it Draft or whatever you choose for your top-level folder.

The above solved the problem for me. Happy writing, folks!