Well, I found a solution that SOLVED the problem on my machine running El Capitan 10.11.6. I hope it helps.
What I noticed is that this annoying problem started along with Safari 10.0.2 and I was told it was not possible to downgrade Safari. BUT I reinstalled El Capitan again over the current installation, keeping all data intact.
I followed the procedures to reinstall which is:
1) Get your backup done
2) Restart your machine and press Command + R during boot.
3) As soon as you get the options to restore from your recovery partition, call Disk Manager and check your OS HDD/SSD verify and to restore permissions.
4) After that, if successful, go to the option and (re)install El Capitain over installed version.
It took about 40 minutes on my Mac Pro 2010 on SSD.
RESULT? Safari came back to version 9.1.2 AND SPOTLIGHT AND POPUP ERROR MESSAGE DISAPPEARED, VANISHED!! VOILÁ!!
Why Safari rolled back to 9.1.2? NO IDEA! But that happened and makes me believe that Safari 10.0.2 is the problem AND it is back again on my App Store asking to be updated! NO WAY. I will skip this Version of Safari or wait a real bug fix.
I hope it helps someone. Feedback appreciated!
Cheers from Brazil!!