Earlier quoted context omitted.
MacOS apparently caches directory views somewhere, and I can routinely get the "Downloads" folder to not actually show what is in the Downloads folder; often having to resort to "open" on the terminal to access the file. I wish I knew how to force it to refresh the actual contents instead of reading it from the cache.
Do you have that folder set to sort by something useful like “date added”? Then it should work. If you have it set to not sorted then maybe the file is lower on the list and off screen. ~\Downloads is always the first tab in Finder for me and I almost always keep it to show the most recently added files at the top.
The other weirdness is sometimes a file gets updated (think "touch") and it won't change it's order in the list.
Most of the time it works fine. It's like inotify or whatever sometimes doesn't fire.