My comments in blue below:
ChengHe wrote:
I have an iPhone 6 plus with 16Gb storage, yet when I look in the settings there are only a bit over 11GB? My 5 shows 12.6 GBs, not unusual.
So I go to Settings > General > Usage and when I look under Storage, it says Used 11.4GB, 77.7MB Available. Is there some storage missing? Yes, see the article below Is this because the storage space used by the IOS is not displayed? Yes, that is correct.
Connect your phone to iTunes, select the phone icon, look on the Summary Page and at bottom there will be a usage bar. Look at a category called "Other". If it over 500 MBs or so then check out the first link below, it will explain what it is. If you then want to decrease the size do a Restore as shown in the second link.
http://osxdaily.com/2013/07/24/remove-other-data-storage-iphone-ipad/
https://support.apple.com/en-us/HT201252