Previous versions (or shadow copies or file history) take up space: NTFS has the feature of shadow copies of files, which takes up space not counted in the plain file size.
This takes up space, I'm not quite sure where on the file system. Contents indexing takes up space: if you open the properties dialog for a partition, you can see the option "Allow files on this drive to have contents indexed in addition to file properties".You may be forgetting to count the recycle bin which is a special case of hidden and system files.You may be forgetting to check system files: make sure you have "hide protected operating system files" disabled.You may be forgetting to check hidden files: make sure you have "show hidden files, folders and drives" enabled in Windows' file explorer options.
You can see the difference by comparing "Size" and "Size on disk" numbers after opening the properties dialog of a file in Windows' file explorer. Usually the difference is not greater than a few hundred bytes, but if you have many tiny files, that can add up to quite a bit. For example, a text file that contains the letters "hello" has a file size of 5 bytes, but it also takes up space in the filesystem's table to store its name and properties.
OP has already solved his/her problem, but the issue may remain for some lurkers. Here's a comprehensive list of all the reasons I can think of why the used space in a hard drive may be greater than the sum of the file sizes.
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