That's sort of the nature of it? Combat operations over civilian population centers are full of hazards to the population, even if every precaution is taken.
You almost certainly killed civilians with debris over November City in AC5 considering how many aircraft were destroyed. And both AC04 (in the first mission and over San Salvacian) and ACZ (numerous times) see the use of WWII style deliberate terror bombing of civilian population centers.
4 is a little sterile when it comes to civilians, it doesn't often mention what's happening to them. It also will hint rather than saying it, like when it mentions the Eruisan AAA crews strafing the town to shoot down allied aircraft, it means they were hitting civilians.
5 outright tries to clean war up a bit compared to 0, but in all three games you're aware civilians are being killed, as in any war.