Thanks Mark - I was indeed playing it wrongly!
If it helps any, think of is like this.
If an air or naval unit activates to conduct an Action, no matter what it does during that Action, it will incur only 1 Sortie unless it is involved in air/naval combat during its activation.
If it is involved in combat, it incurs the Sorties suffered in combat instead of the automatic 1. Sometimes the combat result is only 1 Sortie so there would not be a difference in that case.