Spotlight can't find apps or folder, only seaches the web
Obviously, Spotlight's index is misbehaving, and you did the right thing using the mdutil command. If repeating that command merely provides the same "Index is already changing state..." result, then the situation requires you to manually remove Spotlight's data directory. It's simple enough to do and it's perfectly safe, but it would still be wise to run a backup before proceeding. Then:

1.) In the Terminal, issue the command

sudo rm -r /.Spotlight-V100


2.) Restart in Safe Mode


Restart your Mac, and immediately after you hear the startup sound, press and hold the Shift key.
Release the Shift key when you see the Apple logo appear on the screen.


3.) Restart (in standard mode) after Safe Mode startup is complete. Spotlight will begin indexing using the preferences you have set for it.