When using the SAVE AS option, the program creates a folder with a number of different things in it, and then the project. If you use SAVE AS again, it has to go into the first file and creates it again. It does this every time you use SAVE AS. Trying to save to the computer and back up to a usb, this is a problem. I hope this can be fixed ASAP. Many thanks.
This is a well documented bug, unfortunately a rather nasty one.
Here’s a reference to it in my announcement on the 21st Nov with details on how to delete the files and dolders afterwards:
Bah, evil bugs. Thank you for letting me know. 
I wish you and the rest of the amazing people working on this the best of luck with getting rid of it.
I just skip the “Save As” since I discovered it does not work properly. I am sure it will get fixed.
Meanwhile, “Backup Project To” works just fine. I don’t bother to zip the files because I don’t have an unzip program. I just keep the project folder intact. I can choose the path where to send my files.
I pre-formed my paths with Windows Explorer first. I have had no trouble.
I have even saved the backup to my flash drive in order to copy it to my portable computers and back again, keeping my work current between the computers.
Hey, works for me.
I am just another Scrivener user.