The reality here, is the only way it can see old files (think there is nothing to upgrade) are for the following reasons
The latest files are not present
Your server is for some reason loading old files (perhaps something like opcache)
As you overwrite any files that exist, it would be overwriting the file which the system reads to see what version it is. So its reading that file and not seeing any updated version. No matter what else is done to troubleshoot there, this is how the system works.