The fact that military objects were located in those cities didn't mean the cities themselves with their civilian populations were acceptable targets. Remember, we were there to beat the Japanese, not act like them.
In the context of the time the fact that cities held civilian populations but would still be accepted as legitimate military targets was a given both due to the inaccuracy of "precision" bombing and general acceptance of civilian causalities. Focusing on trying to create as many civilian casualties as possible per mission was considered "wrong" but again the limitations of the time it wasn't going to be a major factor in planning.
No end of 'evacuate or die' warning leaflets were dropped prior. If the civilian population still didn't heed those warnings after Meetinghouse, well...
While it could be defiance, ignorance or stubbornness, they may not have been allowed to move or may have had nowhere else to go.
I have yet to hear anything about the junta deliberately ordering their civilian population to stay put in the face of the Allied bombings on pain of punishment or similar.
It was considered 'warning' enough that you lived in a city that contained military or industrial targets that could be hit. As to not being able to leave there were of course reasons and restrictions. If you worked in a factory or transport service you probably didn't have an option to just up and leave.
You could probably relocate your family if it came down to it but yes the military/government on all sides of the war tended to "insist" that workers stay in place despite the dangers.
The leaflets were dropped after the first bomb had dropped, which probably would only confuse people further. There was no warning prior, contrary to popular belief.
I believe we have pictures and links to the actual leaflets dropped prior to both bombings. Yes BOTH bombs had warnings issued but as noted they were vague enough that they could be dismissed as propaganda. As far as the residents knew it could be a firebombing attack coming as warnings were given for those as well. The Japanese government and military actively surpassed the news and knowledge of the bombing of Hiroshima and stated it was a "standard" firebombing attack.
The man who survived both attacks in fact was specifically told he'd be arrested if he said anything about the attack on Hiroshima...
Even after eighty thousand people dying in one night back in March?
Your nation is at war and the enemy can bomb you on a regular basis, it's hard to grasp these days but you simply lived with the chances for the most part.
Randy