It wasn't the Aegis system at fault for shooting down that Iranian airliner. It was a whole chain of circumstances and mistakes culminating in an almight screw-up by the captain and crew. In fact they weren't even able to engage it for a couple of minutes because they were panicking so much they failed to put the fire-control password in correctly a few times.
Aegis does have auto-targetting because it was designed to deal with saturation missile attacks on carrier groups - but to shoot down one plane you'd probably be operating it by selecting the target yourself.
The Iranians should have re-routed their civilian aircraft away from a combat zone where their military forces were engaging the US Navy in international waters. But it was possibly the Republican Guard freelancing, so they may not have bothered to tell the rest of the chain of command what they were up to.
The Vincennes gave unclear radio warnings, which the Iranian aircrew didn't realise were meant for them. And the captain and radar crew misinterpreted the flight profile of the plane and seem to have panicked themselves into believing it was an attack profile, when it was just climbing up to cruising altitued as normal.
Biting the hand that feeds IT
