New users can't see Apple applications from Utilities folder in Launchpad
I don't know if this is a related cause and the potential fix but I was able to get the issue resolved for me.

I use Homebrew Cask and I have it setup to symlink the applications from my Homebrew Cask directory into my /Applications/ folder (the default is ~/Applications).

The solution for me was to remove all of the Symlinks (I just moved them to my desktop) and then I ran the terminal command:

defaults write com.apple.dock ResetLaunchPad -bool true; killall Dock

After doing this my Utilities folder showed back up and when I moved the symlinks back into my Applications folder everything was back to normal.

If you do have symlinks in your /Applications/ directory or maybe even aliases it's probably worth giving this process a try.

Hope that helps.