"Collateral" is defined in Webster's Collegiate Dictionary (10th ed.) as: secondary or indirect
In the two examples above, the civilian casualties were part of the target; the planners knew the civilians on the bus or in the apartment building would be killed if the attack went as planned.
So what is collateral damage?
When RAF Mossies made a low-level attack on a Gestapo HQ and prison in Holland the plan was to destroy the prison's walls and HQ building. Some bombs unfortunately hit the prison and killed prisoners. Many more, however, escaped certain death at the hands of the Gestapo. More tragically, other bombs hit a school and hospital, causing civilian casualties. It wasn't a given that this would happen, but as you say: war is messy.
But do we want to say it's okay to target civilians along with legitimate targets? I mean, wasn't there an office of the CIA and/or FBI in the World Trade Center? Even if there was, it would never justify destroying the WTC with civilian airliners, by just calling those deaths "collateral damage".
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And, if these questions aren't difficult enough, then there's the case of the Flying Tigers' attack on the Japanese at the Salween Gorge, which resulted in large civilian casualties along with a decisive Japanese defeat. Chennault got Chiang Kai-shek's permission to make the attack on the Japanese column, which was intermingled with fleeing civilians on a narrow mountain road and bridge.
MRPLUTO