The following screenshots both show my iCloud, viewing from Finder and from web. Why some of the folders from web are not there in Finder? May be I deleted them, I'm not sure. Anyway, is it possible to see the missing folders (Keynote/Numbers/Pages/Preview) in Finder?
System Preferences > iCloud > iCloud Drive Options... and check the boxes for
Keynote/Numbers/Pages/Preview makes the corresponding folders appear.
Indeed both file explorers should look same:
Apple has this site for iCloud Problem: Get help with iCloud Drive
Several things are described in the link:
- iCloud correctly activated on your devices ?
- Enough storage ?
- latest Versions ?
- Internet connection ?
If those points are fulfilled and the problem still exists, I would take a macOS recovery into consideration. Recovery is easy with macOS and your files seem to be online and secure as the web browser show the files correctly (About macOS Recovery).