How do Axis and Allies air units work?
Air, land and sea units can defend against air units attacking them in the same way they can defend against anything else attacking them. The attacking air units are put on the battle board like all other units, and they can be taken as casualties according to their owner’s discretion. The only exception to this rule is submarines. They are the only units that cannot defend against air units. If air units are attacking a sea zone that contains subs, all successful hits made by the subs must be taken by sea units. If there are only air units attacking subs, then the subs cannot fire back. If a bomber makes a bombing run against a factory, only AA guns can defend against them. Since the bombers aren’t attacking the military units in this case, they cannot defend against such an attack. This may be where your confusion is coming from. Bombing runs are resolved separately from military invasions.