I expanded all the other folders under the filesystem to check if there was anything else in there.
I tried to delete them but the program prevented it since it was running in trial mode. There were 2 JPG photos and 9 MOV videos in there. TouchCopy managed to "see" some files in the "Recently Deleted" folder (which was actually "/DCIM/.MISC/105APPLE/" from the filesystem's perspective). Ok, I just installed TouchCopy 16 (trial) on my Windows 7 PC and connected my iPhone 6 to the computer with the USB cable.
I'm guessing people don't even know they have it until their phone starts showing the "Low memory" warnings. The scary thing is that this issue apparently exists at least since 2014 and Apple still didn't fix it. So now I'm at 1,31 GB of wasted space which I can't recover. I then turned "iCloud Photo Library" back OFF and toggled the "My Photo Stream" setting as well, but nothing changed. The "Photos" app still shows everything at 0 (Camera Roll, Recently Deleted, Photo Stream). It increased from 622 MB to 1,31 GB in a span of 1 or 2 minutes. But apparently it made things even worse since it started increasing the "Photo Library" size (as visible in "Settings->General->Storage & iCloud Usage->Manage Storage->Photos & Camera") in front of my very eyes. Since changing the date didn't help, I went into "Settings -> Photos & Camera" and enabled "iCloud Photo Library" just to see if that made any difference. I have "iCloud Photo Library" disabled and "My Photo Stram" enabled. I had 622 MB of wasted space, supposedly used for "Photo Library". I'm using iPhone 6 with IOS 10.3.3 and setting the date back didn't show any additional photos in "Recently Deleted". The "date trick" didn't work for me either. I went from barely having any room left on my phone to almost brand new again. I hope this works for everyone and that I saved you all the time I wasted searching for an answer myself - only to never find one.
If, like me, you had already cleared out everything from the Camera Roll and "Recently Deleted" folder, you'll smile to see that your "Recently Deleted" folder now has thousands of images back.For example, if today is March 15, 2015, choose August 1, 2014. There really are phantom pictures in there, but the only way to see them and delete them is to: I had already deleted out every picture from my phone, including "Messages" and the "recently deleted" album, etc.
No need to upgrade to more Cloud storage or anything else.
I've been searching for an answer to this very problem for a solid day.