I have a folder monitor set up with a tool that filters for a specific filename to process, then moves the file to a new folder and does the rest of the needful.
(thanks again for that idea, I've since expanded it to refer to a list, with just that path and filename, even added a few steps so it doesn't re-open itself after editing, but that's beyond the scope of this post..

The issue is that when the monitor detects that one file, it will not just move that file, it sometime grabs another (or even two), and moves it to the new directory. It doesn't perform any additional actions, simply moves it along with the intended file, but it happens only intermittently, not every time.
I finally got around to testing a theory today, and moved several PDF files into the same directory as the intended, right as the that file was created, and they all got moved to the new directory.. I believe what happens is that as the files are getting moved in, downloaded, or otherwise created, they are being flagged by the monitor and moved to the new folder for the tool to act on, it's like it sees the one file being created and decides that all files being created in that few seconds are needed to be worked regardless of filename. The monitor moves them, but once they are in the new directory, of course the tool doesn't process them because they don't match filename, and there they languish until I hunt them down..
I have a workaround where I have a second monitor running to watch for the names in the new folder and move the affected files back to where they are supposed to be, but I thought I should bring this to your attention. It's quite reproducible on my end, and I'd be happy to share whatever tool files etc. you might need.