JMA,

As said previously by Mike, preparatory bombing is regulated. There are obligations for the attaking party: not target purposely civilian installations and individuals if there are no military threat or clear objective.
Example: you do not bomb the church where all population is gathered while the defense points are 400 m far away. No military value, no military objective and targets only civilians.
Then if populations do not flee: see Mike. It's the responsability of the defnder to protect them during the assault.

Having people (you know what I mean) that do not make it to the status of prisonner... Well, that happens even if I do tend to think that it should not happen.
After it depends on your objective and mandate. If it is to conduct peace imposition mission and install pacified environment: those peole are probably in your list of targets who have to be arrested. This because you prepare the stabilisation/recovery phase.