Item Database:Ammunition & Charges:Missiles:Auto-Targeting
All this data is potentially out of date, and should be taken with a truckload of salt
"It's been said that these missiles can and will target either friend or foe (hence the name). If you are able to target what you want to shoot however, it will fire at that first."
That taken into consideration, FOF missiles are the least effective of all missiles. They will target what you want them to target 40% of the time or less, will make CONCORD eliminate you if used in highsec, and are almost completely ineffective in fleet fights. It is true they will target what you are targeting(if it is in range), but if you are targeting the ship, you should be using regular missiles.
An auto-targeting missile will typically strike the nearest destructible object. This may include a friendly fleet member.