Update Feb 9th, 2017: MySQLWorkbench is just too buggy for me for too long. The workaround in this article no longer works, apparently. So, I've switched to using Sequel Pro.
I had this issue where I couldn't run any queries in MySQLWorkbench. I updated to the latest version, 6.3.8, but that didn't help. I searched through forums and found something that worked for me. I changed the group of the MySQLWorkbench.app to staff. it was previously set to admin. The command I used was something like the following:
chown [put your username here with the brackets]:staff /Applications/MySQLWorkbench.app
chown loopduplicate:staff /Applications/MySQLWorkbench.app