My take?
A major cock up. No less, no more. The command element of the ship should have been held accountable and USN procedures examined in depth.
The shootdown has nothing to do with beagle's anti US rant however. Don't find ways to connect the dots between a statement from Kerry now, Beagle's often trotted out, decades old whine ago about being challenged and the suggestion that freedom of navigation rights should be stuffed and the ship should return to US waters. You'll be as crazy as him if you do.