The used space on the SSD is much more than the sum of all files on it, how?

Question

I found out that Windows calculates much more used space on my 128GB SSD than the total volume of all files on it. WinDir calculates only 62.4GB even with junction point following, but Windows shows an used size of 87.8GB, 40% more!

I found a few questions on cases like this, but none of them provided the good answer to me:

• Why don't the sizes of my folders add up to the size of my hard drive in Windows?, Windows shows more space used, than actually is and What is the difference between "used space", "size" and "size on disk"? (and some more like these with roughly the same answers):
  WinDir counts the hidden files as well, and I would be really suprised if file indexing took up 40% of the used space... And cleanmgr.exe cleaned up only a hundred megabytes.

• Why does WinDirStat report less space used than Windows does?:
  System protection is turned off as is, so no System Restore files.

What could be the cause? Is there any way to reclaim that 25GB space of mine?

(System: Windows 10 only, 128GB SSD + 1TB HDD, user folders natively moved to the HDD. If you need any other details, ask for it.)

Answer 1

The answer is simple, as @Daniel B pointed out: Run WinDirStat as Administrator. Since I assumed it does so by default, I haven't, so it couldn't count about 25GB file in other users' folder.