Environment:
Mac OS X 10.11.1 El Capitan Bitcoin Core 0.11.2
Problem:
Every time I open Bitcoin Core, I get prompted by Apple's Gatekeeper security:

Temporary Solutions:
Option 1
Specifically remove the app from quarantine:
sudo xattr -d com.apple.quarantine /Applications/Bitcoin-Qt.app
Option 2
Disable Gatekeeper.
Option 3
Edit permissions.
Cause:
I believe the actual cause is the permissions on the file. Bitcoin Core has 0555 permissions, but all the other applications I have installed myself have 0755 permissions.
I verified, by changing the permissions to 0755, opening Bitcoin Core, clicking "open", quitting Bitcoin Core, and opening Bitcoin Core again, and I no longer receive the Gatekeeper security prompt.
However, Bitcoin Core is now prompting me that I "need to rebuild the databse using -reindex to change -txindex", but I'm guessing this is because it may not be reading my bitcoin.conf properly anymore because of a permissions issue that I have caused. Edit: I think this is user error.