No they didn't. The "macOS Applications folder" checkbox is ticked. Going through the macOS index rebuild from Alfred's Advanced preferences, there are no error messages in Terminal.
I saw in another post, about problems finding apps with Alfred, the Alfred metadata tool, so I ran it to check. Attached is the output for the Typora app.
The one thing that I did do prior to installing Alfred v4, was to uninstall v3 using a third-party uninstall app. I don’t see why this should have any relevance, but I thought I would mention it.
Spotlight finds the apps without a problem and Alfred finds the apps that come with MacOS, such as Notes, Mail, Calendar, etc., but not any third-party apps that I have installed.