I deleted the original because it was a bit incoherent.
The problem
When I select multiple targets, more than my aircraft has designators for, the aircraft still fires as many missiles as there are targets on my target list when you press the trigger, and not as many missiles as there are designators. This doesn't really make much sense but you get used to it. I would prefer if it were changed, or maybe a HUD or gameplay setting to change this behavior to another one.
The Solution(s)
Solution 1: Make it so that when you have more targets than designators selected, your aircraft only fires one missile per painted target per trigger pull. This lets you do the normal thing where you press the trigger how ever many times you want to shoot each target.
Solution 2: leave it alone and we can just call this a skill issue.