I am having this problem as well. Not all of my files in the Pythonista iCloud folder is showing up in Pythonista. If I go into the Files app and open the Pythonista 3 folder, I can see that it is only the files that are downloaded to the device (not having a cloud icon next to them) that shows up in Pythonista. If I manually download the files in the Files app, they will then show up in Pythonista.
I really hope for a fix to this bug, since Pythonista is useless to me if I can't trust the syncing to work reliably.