This appears to be an issue for both iPhone 6 and iPhone 6s users in the app display settings for 4.7" screens. I have the exact same issue on an iPhone 6 that I upgraded to iOS 9 and restored a backup from an iPhone 5s via iTunes. Will have to check out iOS 9.1 beta...
I can confirm this. I bought a 6s for myself over the weekend and gave the 6 to my wife. Restored hers from iTunes and she has the problem but I, luckily, don't.