Looks like several instances of backup files or dupes. The names look like scanner-assigned names. In Finder, are there actual differences in the files? Something going on with your scanner?
What this Could be (I’m investigating): when the Scansnap creates the PDF files, it starts out with a temporary .pd~ file. When it’s finished, the file is renamed and ready.
Maybe the script picks up the files before they’re ready!
I’ll add a wait command to the script to see if that fixes the problem.