The answer is simple as well (if a bit tedious) I have found that the iPhone does this from time to time, especially in situations where you don't have a lot of free space to begin with. there are a couple of ways to proceed.
The first I have not done myself but I understand that if you go to the iTunes store and attempt to buy a large-ish movie it will attempt to download to your phone but then report that there isn't enough space allowing you to cancel the purchase. Supposedly IOS will attempt to clear some space to download the movie and you should be left with some free space.
The procedure I have done to remedy this issue is simple. Backup your phone to your computer, download all the Apps too. Good idea to give the backup a password. Doing so allows iTunes to keep the passwords saved on the phone.
Once that is done go into Settings -> general -> reset -> erase all content and settings. And let the iPhone completely erase itself..
Once the reset is complete plug it back into your computer and in iTunes restore the phone from your backup (remembering to select the most recent backup).
This might take you an hour or so but when the procedure is done you should have regained your missing space. How much space will depend on what all you have on your phone. But the extra cruft will be gone, eliminated in the backup/restore.