The third gen 12.9” iPad pro has a USB-C port. If you are using the USB Thumb Drive with no dongle or hub, it must have at least one USB-C plug. It’s pretty common these days to find a drive that has USB-C on one side and the older USB-A on the other. Older Macs will need that, newer ones have USB-C ports.
Lightning is what you use to plug into your iPhone, if you have one. No USB-C iPhones, yet.
That said, since you did not mention dongles/hubs, and it’s the Files app, I can think of only two possibilities. Either there are residual files on the drive that the iPad recognizes as folders, and the Mac does not, or the iPad is keeping a catch of info for the drive that it has not updated.
In the first case you could probably view the hidden files/folder using the Mac and delete them. It’s been a long time since I had a Mac, so I’m a bit fuzzy on where the command is and it’s exact wording, but somewhere on the drive’s viewing options you should find something like “show all files”, “show hidden”. or the like. Look for any files that begin with a dot, and look like they are about the folders you want to delete. Leave the . and .. files alone. If you are familiar with the command line, you can view and delete the files that way, using the “ls -a” command to list all files in the current folder.
Hiding certain files (that begin with a dot) is typical of Linux, Unix, and MacOS which is a version of Unix at heart. These are mostly system files that you don’t want to edit or delete by accident.
If it’s problem on the iPad, then my first recommendation is the all powerful restart. If the cache that is keeping the folder info is in a temporary file, then this will probably clear it. If it’s a glitch, it will clear it. I can’t think of nothing else you can do on the iPad itself other than hopping the cleanup routines eventually catch and remove the ghost directories.
Then there is the simple yet extreme method most support techs would probably use, because it’s less work than figuring it out. Make sure there is no data that needs to be saved off the drive. If there is, save it off the drive. Reformat the drive. There will be no possibility of unseen files on the drive, and the iPad will (probably) see it as a different drive and there for not show folders that only exist (in theory) on the other completely not the same drive.
Well, that was a long winded way of offering three fairly simple (maybe) solutions.