I know this is probably frowned upon here, but if anyone is having trouble with this, I'd definitely recommend giving this free app (Keyboard Clean Tool) a try instead. I've used it for years with no issues.
I typed "sec" looking for something and this showed up in results:
SecurityFixer.app
/System/Library/CoreServices/SecurityFixer.app
I didn't specify this folder to be searched. Is it pulling from the Spotlight index or something?
I unchecked everything in default options & removed all folders form scope but it's still there. Anything from that folder is.
What should I do? I don't want to lose keyword latching history.
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What you were doing when the issue happened
see post
Whether you were able to replicate it a second time by performing the same action
yes, see post
Include the Alfred version & build number you are using
Alfred 3.3.1 Build 806
Include your OS X version
10.12.3