You might have some files hard-linked across directories, or worse (but less likely), there's a directory hard-link (not supposed to happen) somewhere.

For the uninitiated, a hard-link is when more than one filename points at the same file data on the disk. This is not the same as a symbolic link. Symbolic links are special files that contain a file or directory name and the OS knows to follow them to that destination. (And they can be used to link to directories safely.)

Some programs are not hard-link aware and will count a hard-linked file as many times as it sees it through its different names. Likewise they will count the entire contents of a hard-linked directory through each name.

Programs tend not to be fooled by symlinks because it's more obvious what's going on.

Try running a duplicate file finder. Don't use it to delete anything, but it might help you determine which directories the files are in and maybe why it's like that.

Also back up everything important and arrange for a fsck on next boot. If it's a hard-linked directory fsck might be able to fix it safely, but it might choose the wrong name to be the main one and remove the other, breaking something. Or remove both. Or it's something else entirely, which by "fixing" will stabilise the system but might cause some other form data loss.

That's all unlikely, but it's nice to have that backup just in case.