iOS Numbers and Pages turned into folders

I decided to copy my encrypted Vault 1 from iCloud Drive to an external hard drive (formatted AFPS). I created a new Cryptomator Vault 2 in iCloud Drive. Then I opened Vault 1 on that HD and copied it into Vault 2. Now when I am looking at the files all of my pages and numbers documents (Apple format) show up as folders. Did I screw something up?

No, your documents shouldn’t be screwed up but that’s probably the explanation: