Depending on the specific conditions, the autocrew may not pick somethings out... the actual operation of the autocrew depends on the math of the sensor engine, as opposed to the actual 3-d display... so more or less, you can think of it as the crew only calling out somethings when they have a certain confidence... usually it works fine.
That mission, with the blue speed boats, is a bit of an unusual situation... the best bet that I have found is to illuminate them with your Surface Search Radar and then assign the CIWS to attack them. The Vulcan makes nice work of the boats when you get close enough for the CIWS radar system to track them, as they are generally too fast for the Mk92 Fire Control Radar (so no SM-2 or 75mm), too close for the Harpoon to be practical, too far for the .50cal, but *just right* for the CIWS.
Try it, it's very satisfying to watch them get eaten up by 20mm on the Helo Spotting Camera.
PS Generally speaking, the torpedoes on the FFG are for ASW, if you have another ship in your sites, the frigate has FAR more effective weapons than its LWTs.