Paperpile sync does not create duplicate files, at least we have not heard about it in 2 years. Also I can’t think of any scenario where MetaPDF would create duplicate files.
What’s very common though is broken Google Drive sync implementations in other programs. Unfortunately, we’ve seen that repeatedly (e.g. with Goodreader Tip: Sync with GoodReader on iPad). It does not sync the changes properly in the original file but creates a different file with the same name. That might look correct superficially but it breaks everything.
Unfortunately there is not much we can do. We’ve contacted for example the Goodreader developers and they acknowledged the problem last year. I’m not sure if it’s fixed there and I also don’t know about the program you used.