For this warning to show, three things have to happen: (1) You’re on the WordPress homepage. (2) You have a custom layout set to show. (3) That custom layout either doesn’t exist or contains no elements.
I have a feeling you’re just getting some options mixed up. Do you have a “posts page” set under Settings > Reading?
If so, WordPress now treats this as the “homepage” and what you perceive as your homepage is actually the “frontpage” — And so when WordPress shows your “posts page” it’s using the theme’s homepage file and thus whatever you have set under Appearance > Theme Options > Content > Homepage will take effect there.
If I have guessed correctly in what you’re trying to do, there are a couple things you could do to remedy the issue.
Option 1: Go to Settings > Reading > Frontpage displays, and for your “posts page” make sure nothing is selected. Then, make sure your “Blog” page has the “Post List” page template applied.
Option 2: Go to Appearance > Theme Options > Content > Homepage > Homepage Content and select “Posts”
Note: When you do Option 2 in conjunction with a “Posts Page,” the page template selected on your Blog page becomes irrelevant as WordPress is no longer using page template files for that page.