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XProtectUpdater is the system updater. Restart your Mac in Safe Mode. To restart in Safe Mode, turn off your Mac. Turn it back on and immediately hold down the Shift
key on your Keyboard until it boot into Safe Mode. Then open Little Snitch, goto the Little Snitch Configuration, click the + button, choose the application (/System/Library/CoreServices/Software Update), allow any server any port any protocol.
Close it. Then goto Apple > Software Updates
. If that didn't work, disable Little Snitch from there. Restart your Mac to desktop (normal restart) and then run all Software Updates from Apple menu. Then you can enable the Little Snitch back.
Also, make sure you installed latest version of Little Snitch on your Mac. Download and install it from here : http://www.obdev.at/products/littlesnitch/releasenotes3.html
Please let me know if that didn't work, so we can continue troubleshooting. Don't Rate my answer until you are satisfied