That would happen if the folder on your desktop is actually a link to
the one in /home - if you right click on the folder on the desktop and
select 'Properties' what do you see against 'Type:' ?

If it mentions anything to do with 'link' then it's not the actual
folder but if it says 'folder (inode/directory)' then it is a folder
in all the sense of the word.

Do the same for the same folder you see inside /home - and if both are
bone-fide folders then you have some sort of cross-linking going on
which would indicate file system errors. Cross linking isn't good news
but before trying to sort out make a backup of the contents of /home
as fixing may well delete both !

Hopefully one or other 'folder' may turn out to be a link !!