iPhone 6s Plus.
Ok, so I just dealt with this whole same ordeal, I could not find a non-installed app that matched the version number listed. However the method of removal was correct, you simply have to find the app you are missing, even if it's the long hard way.
In my case, the size of the app and the version number were both different as to what was displayed in the Manage Storage area of Settings compared to the App Store right now. I was looking for an app with a version of 3.0.12 and a size of 59mb (google was useless), when I found the app was actually in the App Store as 3.0.1, and a size of 96mb listed. The only way I figured this out was looking thru my list of "Not on this iPhone" apps, and for version numbers that were at least in the ballpark of the one I was missing. The app versions posted are going to be the most updated version, not the one you might have installed and "ghosted".
I also discovered you cannot look at every app's version history as well. Any app that has been removed from your country's iTunes store, you CAN re-download it (for the most part), but you CAN'T see any other information because it's been removed. So I ended up just re-downloading a handful of apps in the 3.0 to 4.0 range, this took awhile yes, but it worked out.
After downloading a few apps, I went back to Settings, the TOP ICON was still a ghost with no name, but when I tapped, instead of saying (null), it had the NAME OF THE APP!!!
So, I didn't DARE delete it right away, I wanted the iPhone to recognize it first. I rebooted (simple off and on), and the Settings page was corrected, the app was in it's proper place with name and icon. At this point, I deleted all the other apps the normal way (jiggles). However the offending app I deleted by using the Manage Storage section of General Settings. This time I could see the name of the app and the icon as well. It deleted just fine, then I rebooted for good measure, and all seems well in the world.
So hunting for the missing app was irritating, but it did work in the long run. This was the only time I've had an issue with an app I simply deleted, all other "ghosting" issues I have had with iOS 9 have been updates that don't finish properly.
I really feel this should be (and should have been) a high-priority fix from Apple's point of view. I've found people that use Auto-Update and they have no idea when apps just disappear from their phone because they weren't paying close enough attention.