Putting the combat system in "automatic" is a little more complicated than that. There are two sets of keys, one at the Tactical Action Officer (TAO) station and one at the Missile System Supervisor (MSS) station. Both the "Fire Inhibit Switch" and "Remote Launch Enable" keys must be inserted and turned. On top of that, a doctrine statement that enables fully autonomous firing must be enabled. This doctrine is enabled by the Combat System Coordinator (CSC), and when such a doctrine statement is activated, several key watch standers, including the TAO, get an audible and visual alert.
When a watch stander has to leave his console, another watch stander takes his "submode", or in some cases moves to his console to cover his responsibilities. For instance, when the Radar System Supervisor had to leave CIC, I would operate the SPY-1B radar until he returned, with the TAO being informed.
As for why there were 2 missiles, there are 2 possibilities.
1. The second missile was fired at the F-18 that was several miles behind the first one.
2. The system was configured to fire a salvo size of two against ASCMs.
As you said, this F-18 was conducting a refueling mission. It was definitely friendly fire that brought it down. We don't know all of the details. We don't know who designated the F-18 a hostile missile track. It could have been another unit operating within the Battle Group's data link, like an E-2C or even a USAF aircraft. Whatever happened, it was all recorded, and that data is already at the Pentagon.
Sticking with dyke fight as the cause.
I'm sure it is and have no reason to doubt your description of how things are supposed to work.
What actually happened is anybody's guess right now -- at least anybody without a serious need to know.
My guess is a combination of systems' failure and human error, and at this point anybody can fill in the blanks with whatever story seems most realistic or quaint.
I'm saying a trip to the head is a PG rated version, but it could be almost anything -- from a shift change to PIF's suggestion of "dyke fight", anything that might distract or confuse the equipment & operators from being able to distinguish Friend from Foe.