Just an update that this problem seems to have fixed itself on my computer. Not sure if it is a 10.13.2 thing, or if as you said the OS needed to finish indexing (though when I had first noticed the problem, it had been weeks since the installation of High Sierra).
I have noticed over the past few updates that when searching for a file using Alfred file search, the results now display alphabetically instead of having the most recent file first. I think this might be related to the line in the most recent release notes: "Fix alphabetically sorting files in Alfred's File System navigation with APFS".
Is there a way to revert back to the previous behaviour of most recent files displayed first? I liked this much better! My apologies if this issue has already been raised.