I just uploaded a new binary to iTunes Connect and added it to a new version of an iOS app.
After adding the binary and saving changes, iTunes Connect displays the warn
My app was reviewed and approved for release, despite this warning message, so I can only assume it's an issue with iTunes Connect.
It now appears in the App Store with "This app is designed for both iPhone and iPad" and the iPad screenshots are shown.
My advice to others is to ignore it and submit your app for review.