Clock icon next to some apps on macOS Mojave

Solution 1:

Bug

Apparently, the icons where caused by an innocuous bug.

After restarting the Mac mini, the icons were gone.

Solution 2:

I think those application are auto downloading any update or one of the downloading process has disturbed previously. Because of that the downloaded status is displayed as a % of the total download with that clock mark. You can see it with your self by simply adding a new download intentionally.