This is an interesting conundrum, and something which is going to take a bit of consideration.
For file search, Alfred uses the macOS metadata for searching, and as you've seen this is returning the Document folders within the mobile document folders for iCloud Drive. Finder is fudging these to just show the application name: For example, with Sketch:
~/Library/Mobile Documents/WUGMZZ5K46~com~bohemiancoding~sketch/Documents
... is just showing as Sketch in Finder, even though it's actually Sketch's Documents folder. This is obviously some extra logic within Finder, which is not applied to Spotlight / metadata.
I.e. You'll see the same "documents" results within Spotlight as you do within Alfred.
Alfred is already doing a better job than Spotlight in this respect, as at a glance, Alfred will show you the source of the document folders within iCloud.
Having said that, even though this isn't technically a bug in Alfred, I've added a ticket to look into what I can do to make this more graceful.
Cheers,
Andrew