I'm having a similar issue. I've got several files with Finder comments and Spotlight is able to find them, but Alfred is not.
I've tried reloading the Alfred cache. I've also upgraded from Alfred 3 to 4. These files are located in /Applications (some are in sub-folders, such as /Setapp, but not all)
Any suggestions? Thanks!
Here is the output from Alfred Metadata Tool: https://pastebin.com/ePm0UheM
Below is a screenshot showing comments, Alfred, and Alfred Metadata Tool.
(link to screenshot: https://www.dropbox.com/s/9fpzjj8pk18d8v7/Screen_Shot_2019-06-10_at_4.21.02_PM.png?dl=0)