macOS Mojave Safari favicons
close Safari
delete  /Users/Daisy/Library/Safari/Favicon\ Cache (insert your username where appropriate)
delete /Users/Daisy/Library/Safari/Touch\ Icons\ Cache
delete /Users/Daisy/Library/Caches/com.apple.Safari 
restart Safari


Now watch all blank icons being auto-filled by Safari after a few seconds. 

This should work unless the websites that the icons you are missing can no longer be retrieved from the web (website is down, inaccessible etc).

Alternatively, you might try to just delete the offending icon (keep the pointer above it for two seconds to get a close/pin control toggled visible), then open the desired page and drag its favicon to a new window with TopSites again.



To find these folders:


Press Cmd+Shift+G in Finder or select Finder Menu > Go > Go to Folder
or just open Terminal and type


rm -rv /Users/Daisy/Library/Safari/Favicon\ Cache

rm -rv /Users/Daisy/Library/Safari/Touch\ Icons\ Cache

rm -rv /Users/Daisy/Library/Caches/com.apple.Safari