It does not look as the hardware should be a problem. In Linux the difference between a hidden file and a normal file is the dot in the beginning of the file name so there are no "hidden files" that could lurk in your /home and not be seen.
This is clearly not right, but I guess nautilus shows the wrong numbers somehow.
Try to pinpoint what part of your /home that has the content - check the numbers for each subfolder (remember hidden files and folders) and study that folder
Don't fix it if it ain't broken, don't break it if you can't fix it