Actually, it's my bad and some issue with the Mission Editor. After looking into it again I found that I actually had put in 2 carriers though I couldn't move the second carrier but clearly the game has no issue with having 2 units in mostly the same location.
I've been thinking about the me being shut down shortly after firing the Sidewinder, I think I might have ripped the wings off of the plane rather then passing the missile. Just after turning on the afterburners I pulled the stick back really hard, this is shown on YouTube to be capable of ripping the wings off. The other incidents where I passed the missile the missile was most likely near hitting the ground while I was still up high in the air. The missile simple ran out of speed and was dropping out of the sky. I tried to mark this is solved, hopefully that worked as intended
Tweety777's post in Essex class carrier, sometimes a catamaran, but I put only 1 carrier in the mission was marked as the answer